You may already know this about using Repetier-Host manual controls: You may not be able to use all of the left/right forward/back manual controls until you home the particular axis. This drove me crazy originally until I found out about homing first. But be careful - until you have the end stops configured correctly (especially the X axis in my instance). your instruction to HOME may force the extruder to the end and then keep trying to move. Also, don't be surprised if one Axis (probably X) is reversed, such that the end stop is for MAX not MIN, and the firmware has X configured as inverted.