Squatting is a pretty natural movement, so (unless you have a medical condition holding you up) it's probably just a matter of practice. I would forget the bar altogether until you could do a full parallel squat. I would just practice with no bar. Or, use a broomstick to get the feel of having something on your back. You can also use a standard bar (15 lbs.) instead of the Olympic bar (45 lbs.) if you gym has them. You'll get there eventually. The weight is irrelevant until you're able to do the movement.
As far as bar placement, that's not so much a big deal. Olympic squats are high bar with a wider grip. Low bar usually transfers better over to other lifts like deadlifting. I think it's a better lift for sports, but it's not a huge deal Do what feels more comfortable for you with setup.
Squatting to parallel is essential though. So, just practice. I'd forgo the squat machines too. They come nowhere close to replicating a real squat.
I have helped several people who had the same flexibility issue. Typically, it didn't take more than a month or so to overcome this issue.
One question I do have though: What's painful about lifting the bar off the rack?