Sorry it's been a week - I've been on holidays and have only been on the internet for a grand total of about an hour in the last 8 days - and I haven't gotten back to you on the addition of squats in stage 2. I've gotten my hands on a copy of NROL4W and have given stage 2 a closer look. I think if you want to keep doing back squats, your best bet will be to do them on workout A, either before squat/presses or instead of them. I'd note that doing them before squat/presses may reduce the weight you can lift in the squat/press to a certain extent, but the squat/press isn't so much about weight as it is about explosiveness anyway, so that's not a biggie.
Since stage 2 has you doing each workout only 4 times, you could just do 2x10 like all the other exercises and try to add a little more weight each time. Alternatively, you could use the same model from stage 1 but decrease reps and increase weight/sets every workout, rather than every other workout. In this scenario, I'd make sure that every time you do squats, you aim for a slightly heavier weight than what you used the last time you did the same number of reps (so, say the last time you did 8 reps was 85lb, this time through it might be 90-95lb).