About a year ago, I used to use the Smithy exclusively for squatting (however, the bros here enacted a virtual seance and exersized the demon of lameness from me...)
While on the Smith, I kept feet closer and toes straight...decent on the quads, but get same thing from safer Leg Press (IMHO).
Doing REAL squats, on the rack and after experiementing different ways, I'm most comfortable with toes out (about 45 degrees) with feet semi-wide (about shoulder width) and just about ATF. Straight back, head level but looking up...I think this form provides better balance; also, while going ATF the quads are outta the way when wide.
You mentioned your knees ached....I usually slow jog about 1/2 mile and really stretch out quads/hams before my leg WO.
Like you, I only use the belt if going heavy....
Really enjoying the 20 rep workouts in the mid to upper 200lbs. Really helps settle in on form also....
Good luck