All you need to do is setup a Windows (XP, for best) and the rest is a simple as setting your virtual xp to hibernation. Whenever you want to put a rom on your Flashboy it is a task of seconds, instead of rebooting you machine, switch to windows, install a game and than reboot to get back on the light sight of things, namely Mac OS.
Note that you will have to choose the USB Port where FlashBoy is connected in the Virtual Box settings and unplug and replug it when XP has booted.
I haven’t tried Fusion nor Parallels. Both feature a good coherend mode where windows runs transparently on you mac desktop. I believe it is eating up way too much resources (RAM, CPU) for such a small task, besides that both cost a couple of bucks. Virtual Box is free, though.