Some emulators support auto patching for .ips files, I haven't used the emulator enough to know whether or not it support its. Although I do know, that if it does support it, the rom and the .ips file have to the same name.
For example:
Japanese_Game.smc
Japanese_Game.ips
Game.swc
Game.ips
Remember it has to be exactly the same, and case sensitive.
Anyways, hope that helps. otherwise just patch the rom before transferring it! It's not like it's hard. Just google ".ips patching" or "Lunar IPS" or "IPSxp".