You gotta sit on the box, not think of squatting down, then shins will naturally be perpendicular. At first it is kind of awkward to think of sitting down on something as you do on a toilet with a ****load of weight on your back, just start light and build up to it. Concentrate on technique, weight doesn't matter in the beginning, don't let your ego get the best of you.
It also takes a bit of hamstring flexibility to sit down properly, so a short dynamic warm-up for hams might help. Also practice the motion wherever you're sitting down on something throughout the day, be it a chair or a seat, keep back straight, stick your ass out and sit down. Same thing for getting up, pretend you're box squatting with just body weight.
Just small tips, hope it helps. Been doing these all summer.