You can do either. You can flash a custom bios (half and half) before putting the switch in, or fit the switch and then flash one half. However, personally i usually fit the switch and then flash a bios. Which means if the flash fails, you can flip the switch to boot your xbox, flip it back and re-flash and fix.
You can place either bios, on either side of the switch. Again, it makes no difference. I would suggest placing the bios you think you will use less often, on the Vcc side of the switch. Applying Vcc to A19 causes a little more heat to be created in the MCPX. Some people suggest cutting the track back to the MCPX. I have just placed a small heatsink on mine. Its been running like that for at least 18 months now. Also try using 3.3v first, if that doesn't work, try 5v.
The ground connections you refer to are all the same. You can use any.
I am no expert in original bios' versions. However if you put the switch in before flashing your bios, you can always do the switch - boot - switch triack again. I think there is a list on the main site, or perhaps in the bios forums.
Obviously, when loading an original bios, you will need to have your hard drive locked, or you will get an error.
I hope that helps.