So I recently got a Prusa i3 reprap printer, and when I click the home button on the Repetier software, my extruder (x-axis) moves to the side where its limit switch will be activated, but my bed (y-axis) moves to the end of the printer opposite its limit switch. Could I have installed something wrong? Or is there a way to fix this issue in the software itself? This is driving me crazy, so a response would be greatly appreciated. Thanks.
You can invert the Y axis stepper direction in firmware, or move the limit switch (the second one could result in mirrored prints if the limit switch is actually where it should be). The easiest option IF your motors have connectors that can be rotated 180 degrees is to just unplug the y axis, spin it 180 degress and plug it back in, this should change the direction it moves in.
Where is the Y end stop mounted?
If it is at the front of the printer then it is a Y max endstop, if at the back of the printer, it is a Y min endstop, firmware has to be configures accordingly.