Well not sure what to suggest in that case. I don't use Repetier-Server.
If the gcode preview is correct, then the software must be writing the correct gcode instructions. Why don't you try printing from the SD card or directly over USB?
Just to check, you guys know you can use the mouse/keyboard shortcuts to move the models interactively on the screen, right? It sounds like that is the realtime method you're looking for. I think that's on page 5 of the Quick Start Guide if you need help with it ("Manipulating Your Model" ...
What firmware are you using? Some firmwares allow you to update these offsets with a simple G of M-code. But most of the time, these options are configured by the manufacturers with the default values hard-coded into the firmware. That way us users don't need to mess with it at all
Perhaps you have already seen this, but there is a nice tutorial on this topic: http://www.simplify3d.com/support/tutorials/printing-with-multiple-extruders/ It sounds like you're doing things correctly though. The gcode preview is actually color-coded based on the speed of the movements. Is it poss...