I use Mareo with EAC to autorip to FLAC and MP3 at the same time. Because it calls the command line encoders it can automatically pass the tags via command line switches so you don't have to worry about it. It's very simple once you get your head round it, message me if you'd like help.
I use Tag&Rename for any other tagging I need to do. Tags every type of file and very powerful and easy to use.
Do you know if there is a tag editor that comes with the FLAC download - I seem to have a couple of files called "tag" but none of them seem to do anything..