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Quick question, when I run the M303 E-1 S90 C3 my extruder starts heating up? Shouldn't the bed heat up with a E-1?

I already did a PID tuning for the extruder and want to calibrate my bed?

E-1 is not the right code. Try P0/P1. Documentation here: http://reprap.org/wiki/G-code#M303:_Run_PID_tuning

If you have any trouble doing PID tuning, try this: http://forum.seemecnc.com/viewtopic.php?f=36&t=11440