What should I do to come back from this running injury?

I went through this spring track season w/out any major injuries thankfully,but after this season ended,I completely broke down. My hip flexor started to hurt anytime I moved,and my knee cap got screwed up. I used to have Achilles tendinitis, and it came back but it went away. My hips have gotten better but not completely and my knees still hurt anytime I bend them/when I try to run.I'm taking this week off of running,but I want to train for cross country so I'm going to start again next week. What should I do?