I was having an issue with my Pegasus slightly over extruding and this added up to quite a mess when printing a few objects.

I opted to do this through Repetier Host because it easily allows you to edit the steps/mm in the firmware. You should be able to get Repetier up and running and this is by far the easiest way I have seen to dial in your extruder.

Open up Repetier, connect to your printer, and click on the config tab at the top of the window and head down to the Firmware EEPROM Configuration. This is where we'll be doing the calibration. You'll notice the first line is steps per mm and includes the x, y, z, and e boxes. We'll be strictly editing the e box but now you know where to edit the x, y, and z as well in case you ever to.

Load your filament into your printer and heat up the hot end. I used digital calipers her but you can use anything you like that measures mm or cm. Mark a spot 100mm up from the top of your extruder and then use Repetier to extrude 100mm of filament. My e steps were set at 90 stock. If your mark doesn't make it to the top of the extruder increase the number, if the opposite is true decrease. You don't want to change this in large increments, try changing it by 1 or 2 whole numbers then down to decimal places to get it really locked in. After all was said and done I had to decrease my steps from 90 to 89.73.

Congrats, you just calibrated your extruder motor!