If you are just taping your kneecap (called patellofemoral taping) It's not going to inhibit your quads from working - in fact quite the opposite: It may help to stimulate your VMO (inner quads). You shouldn't do exercises with pain, but I'm hopeful that once you tape your kneecap you'll be able to do the squats pain free.
The same theory goes for running - don't do it if it's causing pain. Taping your kneecap could allow you to run painfree. If not then try cycling, swimming or aquajogging for fitness. If you can run painfree with the tape then do so but build up slowly and stay clear of hilly terrain for a few weeks.