Yes, it can be quite painful sometimes. Have you seen a physio? If not, it might be helpful in strengthening your muscles to support your joints, and relieveing pain. In the meantime, a few pointers: watch your posture. Slouching throws all your weight onto your ligaments. Also with hypermobility you will be more prone to back problems, another reason to watch how you're sitting, standing and picking things up (crouch, don't bend!) Secondly, keep your knees "soft" when you're standing - not bent, but not snapped back either. Thirdly - swimming's good, you can strengthen muscles without putting weight through them - however, crawl is better than breastroke, which can put uncomfortable twist on your knees. Even if all you're doing is walking through the water, it's neaerly 800 times harder work than walking on dry land, so will help to keep muscles strong. Lastly, try these links:
http://www.arc.org.uk/about_arth/booklets/6019/6019.htm (booklet about hypermobility - print it off and go through it with someone though, as it's a bit medical and mainly aimed at adults) and
http://www.hypermobility.org/teenweb1.htm (info for teenagers.) Hope that helps!