I recently bought the 3rd edition of Starting Strength by Mark Rippetoe. As I read through it I had a light bulb go on when reading the squat section more specifically when he refers to body positioning based on your chosen bar placement, high bar or low bar. Rip is a huge proponent of the low bar squat (I am as well) however a lot of people find this position extremely uncomfortable so they utilize a high bar, which is perfectly fine. In order to make your squat efficient as possible however, you need to make sure you are utilizing the proper leverages. Rip does a great job explaining just how to do this and what your body position should look like based on your bar placement. I decided to take a very little snippet from the book about this subject and talk about it a little more in hopes of helping your squat out. Please keep in mind this is all referring to a normal free squat with a straight bar, not variations there of (cambered bar, safety squat bar, etc.).
To kind of reiterate the point you can observe the pictures below to get a better feel for body position based on bar placement. For more in depth information I strongly recommend purchasing Starting Strength.