Structure the deadlifting and squatting for 5/3/1 like you normally would. On days you would've benched or OH Pressed, do your hypertrophy work then. Not that hard, I'll spell it out for you too
Day 1: Squat 5/3/1
Day 2: Hypertrophy crap (Would've been bench day)
Day 3: Deadlift 5/3/1
Day 4: Hypertrophy crap (Would've been OH Press day)
Advisory: I'm not Mr.Wendler and this is under the assumption you're doing a 4 day split.