I think your problems have more to do with getting the UCB working right than to do with two sided carving. For example, having the carrier roll out of the machine is because the roller did not click when it rolled off the end of the board onto the carrier. The board has to be initially under both rollers when you slowly lower the head until both rollers just barely click. (This is so they unclick at each board edge when they drop the 1/8".) After the board is measured, the head is clamped down the rest of the way as normal.

There may be some confusion about jogging. There are two types of jog. One can jog to determine where the carving will place on the board and/or one can jog to choose where the bit will touch. The operation of the UCB requires that you jog to touch so that the bit can be lined up in the x direction with the touch hole in the carrier side. (normrichards was talking about jogging to place. You should, for now, just use center on board instead.)

I will go and carve a simple double sided carve on the UCB just to see if I have missed anything.