The best thing with FC3000 and Custom Firmware (CFW) flashing into SD card is that entire hardware or stock firmware is not harmed in any way. So you can safely use your Custom Firmware with your FC3000.
And if the ROM files are on the same location: /roms directory on your SD card you can use them for both:
Custom Firmware can be boot using power button. And Stock Firmware can be boot using Select+Power button.
