When I run Fix Common Problems it is giving me an error saying that My SABnzbd and Sonaar should be installed with a different repository.  So my question is can I install from the different repository over the existing dockers?  The reason I ask is that I have everything setup already and working on these dockers and I don't want to have to set everything up again.

It's probably because their respective authors have stopped maintaining them. It's your call whether you continue using them or make the change. I don't use either but when I changed from one Plex repository to another I made notes about the mappings of the old and recreated them in the new. You don't have to delete one container before installing its replacement but make sure the old one isn't running.