will alwaysOn deal with certificates? do I have to do anything?
Since the certificate and permissions are all included at the database level, there should be no reason to re-create the certificate. Always On will take care of transferring the data to the secondary, it should just be there if it's synchronized or synchronizing but matching log block numbers in the DMVs.

If you wanted the certificate to "be" in the "C:\Certificates" folder and constantly use it (not clear as to why from the questions) then it'll need to be on each replica. I'd also say that this would be bad as the keys are on the same server as the databases, which sort of defeats the purpose.