We all, at some point, had to get up to speed on all this. It can get complicated, but it's certainly worth the time and trouble. Your questions are pretty broad, and I think perhaps one of the best places to start is with this page:
http://www.needledoctor.com/Phono-Cartridge-Setup?sc=2&category=2
As for protractors, the following page has several. My favorite is the KWillis protractor. It lets you choose from several different alignment geometries (perhaps the most common of which is the Baerwald):
http://www.vinylengine.com/cartridge-alignment-protractors.shtml
Learn all you can, and things should go well.
-Bob