Mhm. Roms are games so they might belong into the games folder. And a bios is a bios so it might belong into the bios folder. But that's all in the readme. It also depends on the emulator as Wiisx and pcsx-r use different folders.
You can start them through the emulator. And your n64 games don't work right because the emulator is not finished. Did you even read anything about the emus or do you just think they are all perfect?
P.s.: happy 20th thread in 33 days smashtute.
When i'm back from work i'll post a video of me playing frogger on the wii.

 

in the root of your sdcard have a folder called PSXISOS , you can put your PSX images there (cue/bin or iso). I cant remember where the bios files go, but if you search for 'wiisx wiki' in google, that page will explain all, as well as show you the complete folder structure.

You may also want to search for the 'wiisx compatibility matrix' on wiki, that gives you a list of all PSX games tested on the emulator, and any tips/settings/notes to get each game running optimally. Its been a while, but I played FF7 on WiiSX and I remember it ran fine.

Good Luck with it .. :>