The UGC cases don't have a good way to hold manuals, but if you check the 'New NES cases (work in progress)'-
http://www.thecoverproject.net/forums/index.php?topic=17027.msg158458;topicseen#new thread those cases will come with a manual clip. Other than that the best option for holding manuals is in plastic sleeves in a binder like this (I don't like sticking them in the NES dust sleeves because it doesn't protect them as well, it requires multiple dust sleeves for a large collection of manuals, and it looks like junk to store them like that):

If you already have UGC cases you can stick manuals in one that has the tabs cut out. For SNES, you can fit 8-12 manuals in there, depending on thickness. For NES, I used the inside sleeves from a small photo book I found at Walmart for $3. I glued the sleeve to the spine and it worked pretty well. This holder would probably be able to accommodate over a dozen manuals.

