Hi there. The native SNES emulator is generally considered one of the worse emulators on native. Snes9x4D (on Dingux), is way better, and have much higher compitability, and awesome speed, especially when overclocked to 400-430 MHz. I think you'd be much better off with flashing the dual-boot bootloader, put Dingux on an SD-card, and try it out yourself.
In regards to the IPS patching, I've patched Radical Dreamers, and it works flawlessly on Snes9x4D, so other patched ROMs should work aswell.