ajfaull: I just did what you are about to this weekend. It was long and painstaking, but I now have 200+ CD's, ripped via Monkeys Audio format so I'll never have to re-rip these again!
You are correct, you will have to rip these CD's to the *.ape format. Once that is done encode them to *.mp3 or whatever format you want.
I did not have Media Center 11 when I started, but this is how I went about it.
I used CDex to rip the CD's to *.ape files (Monkeys Audio). I was then going to use Monkeys Audio to convert the *.ape files to *.mp3 files. It was then that I found out that Monkeys Audio truncated the ID3v2 tag information. I didn't want to manually adjust the tag information for 2800 songs, so I went searching for a tag editor and that is how I found out about Media Center 11. The trial worked great for creating/modifying the tag information (I liked it so much I purchased it). Once the tags were updated I then used Media Center to create the *.mp3s.
Knowing what I know now, I would have used Media Center to create the *.ape files and then convert the *.ape files to *.mp3.
I was torn as to how to create my mp3's, VBR or ABR. I decided to go with ABR Normal (~192 kbps). 2800 songs took about 15 hours (about 20 seconds a song).
I hope this information helps you, post back if you have any other questions!