I've read a lot on this subject, since I have had massive problems with back squatting, up to the point of almost injuring myself and having to work around them for 6 months.
Wether you should go high bar or low bar depends on a few different factors, but mostly just preference (which you're most comfortable with) and the length of you're femurs.
I am tall with long femurs and have good hip abduction so I do a lot better with low bar and a wider stance, pushing my knees way out to the sides.
The shorter your femurs and the more you can push out your knees to the sides, the shorter the ROM and generally easier it will be for you to hit depth. Your torso will also be more upright which is a plus.
If you're under 6" and have shorter femurs, and don't mind pushing a bit less weight (low bar generally makes you squat more), high bar could be the way to go. Most BBers go with high bar since that tends to stimulate the quads more, although this very debated.
If you don't want to switch to high bar, you can still go low bar for your back squats and do front squats on another day. This is what I do since I need to bring my quad and ab strength up.
Btw, it's anatomically impossible to go true ATG with a low bar position, unless you let your knees travel waaaay forward or use a super wide stance. If you want to go ATG, I would recommend high bar.