a commercial rom is a dump of a commercial game, in the n64's case a special device is used to dump the contents of a n64 cartidge into a rom file. the legal principle is to back up ur n64 cartridges (or wateva console/device/hardware u r backing up). an emulator is a software emulation of a hardware device such as an n64. the fact that u can freely download these emus and its roms implies that u r avoiding paying for the console and its games...or in other words stealing. which is why this msg board doesnt allow requests as nintendo could quite easily shut the site down. non-commercial roms aernt illegal though.
when u do eventually get ur roms (from where eva u manage to find them) u can put them in any folder u wish. in fact u can even .zip (to save space) them and still use them with emus like 1964, pj64, apollo and daedalus. and just choose the directory u store ur roms from within the emu to play ur roms.
