I use EAC to rip the complete CD and generate a cue file.
Then I use MakeAPL from the Monkey's Audio package to generate the APL files.
And, on reflection, I'll just stick with this method. It is very nice to have the individual selections easily available for listening and MC does a great job in transcoding to whatever format I wish for the portable. Here in China, the average background noise is somewhat louder than an anvil chorus. Why have lossless files, take the capacity hit, and hear no real difference?
Plus, I just like the APE format it has a lot of plusses, and with the APL support in MC, it's the best lossless solution for me.
By the way, the APL files in MC are treated just as any selection. I can tag them, add images, analyze, etc. For those with lots of disk space (and who doesn't nowadays?), give it a try when you are ripping new additions to your library.