I can find the length of my rafters using a construction calculator. I measure from the long point of my miter at what point. On the top or bottom of my board?

Top or bottom will be the same length do to the angle of the cuts. As long as you measure from top to top or bottom to bottom and you have your first cut made. I've never seen anyone go from top to bottom or visa versa but with some of the YO-YOs I've worked with, it could happen! I always pull from the top to measue the birds mouth and the end plumb cut if I don't just run it wild.
Also, don't forget to deduct 1/2 of the width of your ridge board thickness from the overall length of the rafters. -3/4" for a 2x. That will allow for the 1 1/2" on both sides.