Here is a link to the instructions for the Team Paradigm "Big Jim Series" Alignment Bar.
That should help explain it a little bit with diagrams. One of the main keys to aligning the brush hoods is clamping the hoods tight to the brushes. The hoods on EPIC motors are slightly too big because the cheapo brushes that come on the brushes are made in Japan, versus race compound brushes we always use such as the 767 and 4499 are made in the US or to US specs. The difference is small, but its enough to make noticable power difference. Without risizing or clamping the hoods, the brushes are constantly shifting back and forth when you hit the throttle.