In fighting a vampire I got a notice I contracted the vampire disease, so I took 2 doses of the cure disease potion. When I went to one of the temples to make sure,the dialogue box told me to repent my sins .How do I know I am cured ? Would mandrake root still work and where would I find it ?

You see it in the Active magics menu

In the Active Effects Menu, look for "Drain Fatigue." If you see that, better run to the chapel, eat or brew something.

If you just have the preliminary disease, not full vampirism, any cure disease type method will work. If you can't pray at a chapel, it might be because of another reason - like you have a bounty or something.

Yes, it sounds like you cured the disease just fine (assuming you are not actually a vampire). The 'repent' message at the altar is, as Leydenne said, a different problem. Either a bounty or your infamy is higher than your fame.