To transfer ownership of a paint horse, do you sign on the back of the papers, or do you have to print out a transfer from APHA? 

You fill out the back of the papers. On my paint papers the sellers name (me) is all ready on there and the buyer fills out the rest of the information.. Thats the way it was done the last time I have bought and looking at the papers I'm pretty sure its still the same way. When the papers are reissued to you then your name will be in the sellers spot.