I have PCOS and have been going to a fertility doc for awhile now. I was on Litrozol and progesterone suppositories and I found out last week that I was pregnant. I ran out of progesterone and the pharmacy was suppose to mail them to me. It has been 4 days and they haven't shown up yet. I have missed 3 full days of progesterone and I am freaking out that I will have a miscarriage. They checked my levels 2 days ago and they were in the 60's. Is my missed dose going to affect me?

How far along are you? A level in the 60's is within the norm, if not above, in early pregnancy.
Have you given your doctor a call regarding your concern? That would be wise as they could provide you with some if they felt it were necessary.