have you put them into the right directory?
/home/pi/RetroPie/roms/snes/
did you restart emulationstation after you transfert the files via FTP?
did you unzip the file if they were zipped in the first place?
in /etc/emulationstation/es_system.cfg there is a defined PATH for roms as well as defined file types for each system, e.g.
DESCNAME=Super Nintendo
NAME=snes
PATH=~/roms/snes
EXTENSION=.smc .sfc .fig .swc .SMC .SFC .FIG .SWC
have a look at yours and make sure the file types are correct, not every emulator copes with zip files (arcade/mame games must be zip though)