Here is what I have learned wearing skirts to work after about a year and a half:
How to make your package less noticeable -
The problem: Yes, men have a bulge, and that's natural. Unfortunately, we live in a silly society that is both uncomfortable with even the hint of genitalia (and even non genitalia, since women aren't supposed to show their breasts). Even worse, men who do things that are seen as overtly feminine are unfortunately seen as perverts and weirdos, and so the presence of a willy tossing around under the skirt, while tolerable in a more enlightened society, has a danger of contributing to this perception.
The solution: I have found that tights, skirt under-shorts (basically, short tights), and compression shorts do a good job of keeping your member in check. At first, I wore compression shorts, but those can be a little thick at the waistband, but still, they do the trick. These days, I either wear skirt under-shorts or tights. I am 6'2'' and ~260 lbs, so it can be somewhat difficult to find them in my size, but not impossible. Walmart is usually a good bet, though if you want to spend a little more money, you can find them at stores catering to plus size women, like Torrid.
Don't try to tie your member into place. Ouch.

Colors and Patterns -
If you just starting out, and you are like me, you suck at color matching. Even when you think you have the hang of it, it isn't uncommon for your wife (or husband) to chime in and tell you how poorly the colors you are wearing match. I swear, sometimes it just seems like everyone's playing a big joke, and no colors actually match. Thus, obviously, I am no authority on color matching, but I can give some valuable advice for beginners -- make sure you have lots of neutral shirts. That includes, black, white, grey, navy blue, and sometimes brown. Make sure you have at least one pair of neutral colored shoes. These are your friends, and will save you from much agony and wasted time in trying to find a top--any top that doesn't make you look (or at least how you think you might look) crazy.
Try to find solid-colored skirts. Patterns are tricky. If you want to wear a pattern, but you are inexperienced, wear only one, and then a neutral. Avoid combining non-neutrals with patterns until you are more experienced, and avoid full body patterns.
The same goes for texture, especially for shiny fabrics. Please, for the love of god, don't wear a shiny shirt with a shiny skirt (at least not until you have a better fashion sense).
How not to look so top heavy -
The problem: You put on a skirt, with just an undershirt on, and look in the mirror. So far, so good. Then, you put a button down shirt on, which you expected to look amazing. Then, you look in the mirror and behold that you have transformed into Shrek.
The solution: If you are like me, not only are you very rectangular, which is not the shape skirt designers had in mind, but you also have a bit of a gut that you don't want to draw attention to. I have found that to counteract this, I need to wear tops that look slimming. Here, we can turn to conventional fashion advice. Dark tops do much to slim you down, however, they are not always necessary. What you need is a shirt that does not hug your belly. Make sure that the shirt accentuates your shoulders and flanks. It should not be too tight, but it should not be baggy either. And, if you are overweight, avoid accentuating your belly. That probably means avoiding tucking in your shirt. Now, I am aware that some members always wear their shirts tucked in. Please don't take this as criticism. I am just saying that if you are a newbie, tucking in your shirt is probably best left until you have a better fashion sense, since it draws attention to your midsection. Also, I know it's tempting, but don't situate the skirt waist at your hips so that your belly hangs over it. Situate it at your waist, where it was meant to be worn. Not doing this makes you look sloppy and leads to what I call front-biasing of the skirt, where the front of the skirt hangs lower than the back.
Best types of shirts to combine with skirts -
The wrong kind of shirt can, again, make you look sloppy. Remember that men's shirts were tailored without any consideration for skirts.
Fortunately, flat-bottomed shirts don't suffer from this limitation, and usually work with pretty much any skirt. The flat bottom complements the skirt hem, and is unobtrusive. I don't recommend tucking your shirt in unless you are thin. It is likely to make you look top heavy. Tee shirts that aren't baggy work surprisingly well with skirts, and can even look unexpectedly professional, especially if they are long sleeved with an undershirt worn under. You also can't go wrong with flat bottomed sport shirts and polos, assuming that they fit well. Sears is a good place to find these kinds of shirts.
Variable hemmed shirts are trickier, and I haven't entirely figured then out. If you want to wear a variable hemmed shirt, try to find one that is meant to be worn not tucked in. Gap is a good place to find these kinds of shirts. Never wear a shirt that is meant to be tucked in, out. It looks sloppy. This is why I avoid wearing dress shirts with skirts. The only thing further I can recommend here is, in shopping for variable hemmed shirts, bring a skirt with you so that you can see the full effect in the mirror in the dressing room.
As a rule of thumb, your skirt should be the "biggest looking" part of your clothing (to avoid looking top heavy)--or at least as big as your shirt, even if it physically isn't. This translates to scaling your shirt with your skirt. For long skirts, you can get away with wearing thicker or larger shirts, and wearing more layers. For shorter skirts, thinner or smaller is better.
Don't try to compensate for your "reduced manliness" -
This is counter-intuitive. We might feel that by wearing something manly on top, it might counteract the "femininity" of the skirt we are wearing on the bottom, but don't do it. It doesn't work.
There are a few reasons for this. First, by trying to look too manly on top you risk looking top heavy. Second, manliness and femininity are not additive. Adding more of one does not necessarily counteract the other (though it can). To see this, simply imagine wearing a frilly tutu of organza, and now try to think of the manliest top you can put on. Not only does it not reduce the femininity of the tutu, but it also looks preposterous, which brings us to the third reason - consistency. I think people expect consistency in your expression (which is likely why it is so frowned upon to wear mismatching patterns and colors, come to think of it). Having a manly top and a feminine bottom creates dissonance.
Now, please don't take this as me suggesting that if you are wearing a taffeta number on the bottom, you should throw on a taffeta top, as well (though, if you can figure out how to do that, more power to you). Rather, I mean shift your thinking. Don't think in terms of counteracting. Think in terms of not "overdoing it." That means the safest bet is wearing a gender-neutral top.
So, what if your skirt is flouncy? If you are worried about your "man card" (ugh), then I suggest not wearing a flouncy skirt to begin with, but if you really do want to wear one, wear it confidently, and proudly. That means your shirt is secondary to it. By attempting to "counteract it" with masculinity, all you are doing is showing how self-conscious you are.
Skirt Length -
This is really a corollary to the last section, but is important enough to mention by itself. Longer skirts are safer to wear (assuming they aren't patterned) because they compliment more male tops. But wear whatever length floats your boat. Just make sure the top you wear doesn't overpower it.
Shoes and Socks -
On, this topic I can't really offer a good reason for any of my preferences, so I will just state them, and leave it at that.
I think it looks best when my socks aren't too visible. For some reason, socks that are too visible paired with a skirt look awkward, and give an appearance of nakedness (counter-intuitively). I don't know why this is, and I also don't know if others feel this way, but I am just putting it out there.
Tennis shoes are risky to wear with skirts, and can easily look sloppy. I suspect this has to do with the fact that skirts are considered "dressier" than pants. Boat shoes work well, but only with nearly invisible socks. Boots work well, and you can wear slightly longer socks with them. IMO, up to the knees, the taller the boot, the less risky it is to wear.
Legs -
If you are not going to wear tights or long skirts, shave 'em. I know, I know. We're men, and men don't shave their legs, yada, yada, but men don't wear skirts either. Society has certain expectations about the ensemble you wear. Obviously, we are subverting this somewhat by wearing skirts, but not shaving your legs with a short skirt, in this society, makes you look sloppy (though, I would guess that this doesn't apply to kilts). Hairy legs with a short skirt makes society less likely to accept male skirt-wearing, not more, simply because society thinks it looks bad to begin with.
Look at what fashionable women closest to your size wear, and look at what Metrosexuals wear -
Take advantage of territory that's already been explored. Obviously, women's figures are likely going to differ from your figure, so not everything will work, but some things will. For example, anything concerning the the legs up to the thighs will probably apply to you, as well. Women also come in many different shapes and sizes, and, fortunately, there are now places like Torrid that cater to women whose bodies don't satisfy conventional (and often unreasonable) standards of beauty.
The same goes for metrosexuals. While they don't wear skirts, it isn't uncommon to find them wearing things women are likelier to wear than men. Try to apply their fashion sense to your own.
Finding affordable, but fashionable skirts -
Burlington Coat Factory has an excellent selection of trendy plus-size skirts at reasonable prices.
Well, that wraps it up for me. I hope to hear some other's tips on this subject.