How to empower my garbage knees?

In just about every workout I do, it's my knees rather than my muscles that limit me. As Im training for a 5k, I'm working so hard to strengthen the muscles around my knees but still struggle to do a few squats without twinging my knees. I think I'm fairly hypermobile, so I'm worried that's part of it too.

What do you guys do to keep your joints strong and supportive?