I use Allbreedpedigree, provided the pedigree is correct (I had to do my mare's twice after double-checking her papers, so she went from 86% to 90%).
The way I do it is start with the farthest name right at the bottom (ie, great-great-great granddam). A foundation QH is considered any QH born before or during 1940. So..say a horse is born in 1942, but its parents are both born in the 1930s, it would be 100% FQH. However, for any TB you find, they're 0%, obviously. So like Poco Bueno x a TB mare would equal a 50% FQH foal.
For example: Doc Bar Doc Bar Quarter Horse
He is 75% FQH.
I did this with my Paint mare too because the majority of her Paint side are actually cropout QHs, in which case I just counted every tobiano as 0% because tobiano does not exist in QHs. Luckily, the colors on hers were all listed and most had pictures to verify.
I usually just screen cap the pedigree and paste it into MS Paint, typing in the percentage of each horse as I go along so I don't forget, the just calculate it all.
Does that make sense?