Should I just endure the pain I get while jogging, or stop and hope to recover?

Well, I have asked previous questions about jogging and running etc. I find that when I run or jog for exercise, I get a burning sensation in my knees and they feel exhausted.

From my previous questions most will tell me to not run for exercise… but the problem is, I’ve realized that I will NEED to run! I’m practicing and building up my endurance because I’ll be doing a military training thing this summer and they told me to start running, since there will be lots of it. I’m pretty terrified for whatever I brought upon myself (joining the military), but I will stick with my plan and go through with it.

So, I plan to ask a doctor and see if they know what’s wrong, but my doctor is out of town for a while… so for the meanwhile, should I just suck it up and endure the exhaustion my knees are feeling, or should I just jog till it burns and then stop to rest? Does anybody have any helpful suggestions of how I can overcome this?