Try running 5/3/1 as it's written - 10lbs per month increase to your training max.
If you want to squat twice a week, you could throw them in 5x5 @ 70% after deadlifts, and do your hamstring assistance on your "main" squat day.
EDIT: just saw Mike already made my suggestion... see great minds think alike!
"Ignore the pain." - Vince Urbank