the key files in the incomplete folder are the downloads.dat and downloads.bak. Think of them as the master index that LW uses to keep track of the progress of the incomplete files.
So, if you want to try using ONE of several "Incomplete" folders at a time, just make sure the dat and bak files are also included with whatever set of incompletes you would like to try to resume.
btw--if this causes problems (incomplete files have a limited life as set in your options), be ready to just trash the incomplete folders: LW will create a new one if necessary. Generally it's not very useful to mess with the incompletes--just much better to start fresh.
--All subfolders (except those called "Incomplete") are shared.
--wishlist: try and see. Sounds like you are having fun with all the power of LW. Enjoy while you can because I suspect LW will start getting more streamlined and much of the power will not be a visible in futeur releases.