On average, the hamstrings are ~1/2 to 2/3rds the size of the quads. Since the quads are a much large complex of muscles (it's actually a group of 4 separate muscles) they are naturally stronger.
As far as exercises go, the squat is primarily a quad-glute exercise. It does work the hams, but only as a stabilizing muscle... the overall stimulation on the hams is not that great. It's a similar deal with leg presses... which work the hams a little more than suats do, but it's still not a lot of work in relation to what the quads get.
For your workout I would suggest alternating squats and leg presses (if time is a factor) from workout to workout and replacing this exercise with another one for hams. Stiff legged/Romanian deadlifts are a personal favourite... but, things like single leg curls, seated leg curls, etc are useful as well.
A personal suggestion... not to contradict medical advice... but, the leg extension can potentially be one of the poorest exercises going if you have a Knee problem. The long story involves a discussion of closed chain vs. open chain movements... the short story is that the human knee joint is not properly designed to support/lift a load that's placed at the ankle. Anyway, be very careful with these. One of the main keys to this exercise is to never "roll" your knee as you lift the weight.
Andrew |