The switched were so the "mod chip" would be "turned off" when both switched off.
Otherwise if you tried to flash the onboard bios with the modchip on, there would be contention on the Address lines and it could not flash properly. I just ripped mine out after flashing.
(After pulling the modchip)
You might want to take those switches and have them toggle the onboard flash ability so you can leave it disabled normally, incase someone writes something bad for the Xbox that tries to mess up the bios. You would not be effected if you left the switches off normally unless you were going to upgrade to a newer EvoX bios if one ever came out then you could just turn them on for that, then back off after finishing.