Do any of you Martial Artists know how to fully recover from a knee injury while still training?

Back in early September I injured my knee in a pro football/soccer trial, ever since then I cannot run more than 1-2 kilometers without needing to rest my knee for 3+ days (I can barely walk then). The part I find odd is that I can kick the heavy bag pretty much all I want without ever feeling pain, I can also roll in BJJ and spar in boxing just fine.
Obviously I can still train as long as I don't run, but I want to be able to run to improve my cardio, because I'm used to running pretty much every day between 6 or 16 kilometers.

Do you guys have any tips on how to get back to normal?