I don't encode directly from EAC. Here is what I do:
1. Rip album to WAV via EAC.
2. Use the front-end included with flac to encode WAV to flac.
3. Use Tagger (which is a front-end for tag.exe) to tag the flac file taking information from the strucure of the file and directories. (Artist - Genre/Album - Year/Track Number - Track Title.flac)

Hope that helps.

EAC (http://www.exactaudiocopy.de/)
flac (http://flac.sourceforge.net/download.html)
Tagger (http://tagger.boereck.de/)