First of all, please forgive me if someone already posted this or it's common knowledge. Search did not indicate it, and I think it's useful option especially for those who RP and want some more choices in their look.
A. How to wear any Formal top with any uniform pants and boots:
1. Create desired bottom look in your main uniform window.
3. Go to off-duty creator and select any formal top, save again.
4. Go to clothing editor section (skip head/body editors). Load your uniform. You will notice that pants carried over from your uniform, while shirt changed to one you have on top of your drop down list.
5. Hit Reset All Upper Body Options button for shirt.
6. Adjust shirt colors and type.
7. Hit Save (if you want to edit it later), then Purchase. Enjoy your new look!
B. How to wear ANY bottom with uniform top:
1. Create desired bottom look in your off-duty window. For 21st Century Formal you have to also choose formal top, do so.
2. Adjust colors. This may be tricky to do, since you can't directly see how it will look later. Just play around. If your uniform turns out grey, go back to off-duty editor, set colors of your top, change top type several times (Formal 1 to Formal 2 to Formal 3, then back to Formal 1). Save after this and try loading in uniform editor then.
4. Go to uniform creator.
5. Go to clothing editor section (skip head/body editors). Load your saved formal clothes. You will notice that bottom carried over from your off-duty clothing, while shirt changed to Starfleet - A - 1. Note that you will have no combadge.
6. DO NOT TOUCH any setting. Just hit Save (if you want easy access to it later) and Purchase. Enjoy your new look!
C. How to create different combinations (only works with 21st Century Formal set):
1. Go to off-duty clothing editor.
2. Select Formal top.
3. Hit Randomize All Lower Body Options until you get satisfying result. Note that color palette for bottom is quite limited.
4. Adjust colors of your top. Do not change it from Formal to anything else, or you will lose your bottom.
5. You can also save your bottom result and use it in uniform, as per point B. Again, you will have to play around to adjust colors. it's pretty random and you will get grey top most of the time.
Got it to work! Took a couple tries 'cause it kept screwing with my pose and hair color, but enough wrangling got my female alt in leather pants and a "tank top" for her off-duty outfit, which looks pretty nice. Not as much to do on the male side, unfortunately.