So, after doing a little bit of research I decided to encode to AAC for my Ipod. But, I don't like the way Itunes arranges the files and I have some old, rather beat-up CD's so I was excited to see that EAC can use the Itunes encoder through Itunesencode. But, for some reason Itunes won't recognize the files or play them. Or even attempt to. Here's the specs:

Itunesencode 46
EAC version v0.95 beta

commandline: -e "AAC Encoder" -a "%a" -l "%g" -t "%t" -g "%m" -y %y -n %n -i %s -o %d

any ideas?

WHOOPS! Figured it out. Had the tagging option on. I found another post saying that ID3 tags don't work so well with AAC files, and that EAC will try to do it all the same. It's very obedient, even to the destruction of your files.