For me it depends on the game console.
NES: I just put the manual in with cartridge in the black dust cover.
SNES: I just lay it on top of the cart, it may be "loose" but the manual is almost the same XY as the UGC so it doesn't move around. The downside is it can put a slight (and i really mean
slight) crease in your manual over time since it can bend around the cart due to gravity. It hasn't caused any noticeable damage to my manuals yet.
N64: Same as SNES (the manuals are the same size)
I don't like the idea of putting the manual in the plastic sleeve/insert of the cover. It can really stretch out the cover sleeve and the cover can fall out of place and you'll eventually have to replace the UGC. I've never tried hot gluing in tabs before as you suggested but thats not a bad idea if you can do it right. If you do this let all of know on the site how well it turned out.
