Just discovered NSUI43DS (and YANBF) this week, truly spectacular. Took me only a day or two to get my faves up on my system, though sadly even though I have a New 3DS XL the SNES Virtual Console doesn't work (at least SNES9x is working).
Gradually going through each game to give them a premium polish, with custom border images and better banners than can be found in the database, and can't seem to find any methods to include manuals. Has anyone been able to figure that out? I saw a guy earlier in this thread had managed to extract them from VC titles, but without luck on injecting them. So many old games benefit greatly from having the manual accessible like that.
Also, if Asdolo ever updates the tool again, it'd be sublime if we could get Game Boy games under the Game Boy banner to load with the GBC Virtual Console, so we can have both the proper colored Pokémon cartridges and GBC-based game color palettes instead of the global preset schemes.
Edit: I found a description of 3DS-rom-tools from ihaveamac on github while searching, doesn't look like there are any tools to automate the process and even if done, it seems to be untested. (Since I'm too new and can't post links, here's the rest of the github url.) /ihaveamac/3DS-rom-tools/wiki/Rebuilding-a-game-or-application-in-.cia-format