I use Pcb-gcode in eagle to make my files. Therefore, I flip the board such that the bottom X0,Y0 is located on the lower left corner of the board and when flipped to to the top, the SAME corner of the board is on the lower left of the board.
So make a fixture to hold the board and then you can locate the origin points for each side. I make my bottom fixture location as G54 and the Top as G55 and thus have two different origins.
Hope this helps.