I know some of them do not go by PTCAS entirely. I applied to UTC and UTHSC in Chattanooga and Memphis and both of them took the higher grade and didn't average them. However a lot of them do (I know UAB in Birmingham averages the grades). I would like check individually with the schools you are interested in and they will be able to tell you. Good luck and hope this helps.
Some schools require that you send a copy of your transcripts, so that would help. Also, some schools require you fill out a secondary application which might include a paper that lets you state prereqs you've retaken with the corresponding grades. This is all something you will need to check with the school. GPA isn't everything so don't stress too much, and if you're really worried, just focus A LOT on other aspects that will strengthen your application.
