hackskii

I use the smith machine some times for shrugs.
I do notice alot of guys use it for their bench, incline and military presses. I know that they use it because the bar is counterweighted or something the bar feels like 0 lbs. So the guys use it for bench when they cant do a plate on the bar. So they use the smith machine and use like a plate or so which would be really like 100 lbs.

I do use the smith machine sometimes for behind the neck military press. I do them really slow and deep but this does bother my shoulder some but gives it a good pump.

I would not use the smith for squats as you have a natural groove and you wont follow that groove following the path that the bar is going. In fact if your bar does not follow the path then your body will and this is just asking for injury.

I would use the cage (when you heal up) go light and get some good form down. Have some guys watch you that do squats and have them tell you what you are doing. It is hard to look into the mirror and see what you are supposed to be doing because you should be looking up while squatting. Have a mate check your form.
You can use the bars to make a stopping spot for the bar and you wont have the problem you had before.

You will get better legs with the free weight than the other anyway.

Hope you get better bro.