Right....
Ignoring clipless completely to begin with:
MTBing is generally much more stressful on knees than road biking, however you ideally want good knee support from musculature to maintain efficient pedalling and keep yourself free of injury.
The key is to learn to maintain a higher cadence, this really helps to further protect the knee. Most beginners prefer to mash a higher gear as they don't yet have the fine motor control to pedal in smooth circles, so everything begins to get worse.
On the road, your ideal saddle height is the one that provides smooth knee motion throughout the stroke, with no acceleration or slowdown through the dead-spot where the cranks are vertical. However, on mountainbikes, whilst the optimum height is the same you generally run the saddle a little lower to enable you to move around on top of the bike, the more extreme the riding you're doing the lower the saddle will be.
Saddle fore-aft is also critical in protecting the knee, as a good starting point you want the front of the knee over the pedal axle when your cranks are horizontal. Whilst this is a rule of thumb, it will get you into a good starting point.
Clipless pedals are a huge kettle of fish and I'd really advise a professional fit for your first set.
With your positioning problems currently, i'd pop into your local friendly bike shop and ask for some advice. Most will be more than happy to assist a novice cyclist in getting comfortable.