Here's the first thing: high bar, low bar and front squats are all different movements. Sure, high vs low bar aren't as different to each other as front squats, but they're still different. You say you're not particularly experienced, so right now you'll benefit hugely from getting good at ONE of those squats. So, pick one and run it for at least a full BBB cycle.
How to chose? Well, IMO you'll be better off with either high or low bar. That's just personal bias though. If you're not a powerlifter there is precisely zero need for you to squat with the bar on your back.
Here's the second thing: again IMO but forget about high vs low bar. A squat with the bar on your back is a squat with the bar on your back. Yes, how high or low the bar sits will have an effect on how upright your torso is and what muscles do the most work. But, so will how wide or narrow your stance is. So will where you point your feet. What is really going to determine how you squat is your body. Bottom line? Find the stance and bar position and foot angle that suits you best and focus on getting really, really strong with that squat.
A good place to start I find is bar sitting just below the tops of your shoulders, just around where the acromion process is (knob on the rear of the shoulders) with feet a bit over shoulder width apart and toes pointing slightly outwards. Lean forward just enough to stop the bar rolling down your back.
I'm not saying that's the best combination for you - it may not be - but it is a nice middle ground.
Don't mess around the with BBB template. Follow it EXACTLY as Mr Wendler wrote it and eat like a horse. Do that for a full cycle using that one squat you picked. At the end, then you can decide whether you want to repeat with the same squat or change it around. The one thing for sure is that you'll be a) bigger, b) stronger and c) a much, MUCH better squatter than you are now.