I'm not familiar with the PC emulators since I stick to the real hardware, but I think you can just load it as any other rom, and then hit the Run button to start the CD.
In Magic Engine, you set the path to the system cards in its configuration file, which allows you to boot from more than one disc drive (logical or virtual).
Though on second thought, maybe there isn't a separate Arcade Card option, considering it's just additional memory and not a different bios. If I was at home, I could check the configuration file, but I'm not.