Do you know what map is on the PFC? - If it's a standard map, or at least one for standard components, it will work until you can get it remapped for your setup.
Obviously if it's been set-up for 720cc injectors and a GT3076... and you've got a standard car, it won't run at all.
I think there may be a "reset to default" option, but your best bet is probably to leave it until you're ready to map it correctly.