<p>I have a prusa 13 that's shipping in the mail, and I intend to make good use of it, one also own a da vinci jr. and the one time it got so clogged that the extruder itself was filled with pla, with that said I replace the extruder, for the da vinci, but besides that, as for my a prusa, what should I do if the extruder, not the nozzle gets clogged that badly?</p>

From an electrical standpoint, a two-phase stepper motors (what most 3D printers use) works the same backwards and forwards, the phase just reverses.  If you are stalling on only one direction, I would look to see if you have a mechanical bind in that direction.  Generally a wiring issue will cause the motor to either not run at all or to run in the wrong direction.
A few things you can check:
Decouple the motors from their mechanical load and confirm that they all run correctly when they aren't driving a load.  If you can't do that, disconnect them all then connect a spare motor to each cable one-at-a-time.
Turn each of the axis with your hand and make sure it turns smoothly throughout the entire range in both directions.  Note: Some times a binding issue is acceleration related - a loose frame or coupling can cause this.
Monitor the supply voltage to make sure that one of the motors is not pulling the supply down causing all the others to stall.