Injury or Wuss?!

How do you know when to run or when not to run when you are in pain? Ever since changing my shoes my knees have been almost too painful to walk on never the less run on. On my first run in the pair of shoes i returned my knees hurt but just a twinge of pain. The assistant in the running shop said that's normal for the first few runs and will go away after 3 - 4 runs. The second run I did in my new new shoes I was in so much pain I had tears in my eyes and thought I should call my hubby to pick me up but decided I was being a wuss and it won't improve unless I got my legs used to my new shoes and running style. So I left it a few days and went out for another run after my legs started feeling better and this time it hurt initially but the more I run the le it hurt. It gets under me knees when my feet impact the ground so I think I was running in a way to reduce the "bounce" and the amount of impact on my knees but now three days later I  struggling to walk an get up and down stairs and am giving my run a miss today for the first time since starting C25K. I will wait for my knees to feel better and recover then go out again to see if it improves, if it doesn't I'll pay a visit to the docs. 

My question is how do you know when your pain is just your body adjusting vs when you have inflicted damage to your body? It's a tough call knowing if you are being a wuss or you have simply pushed yourself too much and need to recover!