yeah, it woulde to be a toggle switch, so when the switch is down it closes the two pins that are normally closed and when its up it closes the other two, but it can be done.
I wouldnt recommend it though. For one thing, im not sure what happens if you turn it on with the jumper in the wrong position, or if you switch it while its on... but i dont think its a good thing.
one other thing... flashing the bios is when you update it to a newer bios version... what your talking about is clearing the cmos (i figured by your title you wernt really sure on this).