I have an answer for you guys. With EAC, rip with compression on, using the APE dll (NOT "external compression"). That will automatically generate a tag. If you let EAC get the track info from freedb, you'll have the added luxury of having track info included! (I find freedb to be at least as accurate as CDDB.)
EAC will slow down a bit because it's compressing on the fly, but it's still faster than ripping to a wav, then compressing it (which doesn't write a tag).
If you want to modify the waveform with an external editor (which I can only imagine in the rarest of circumstances, because the MJ editor is very, very good), do the following: import the *unmodified* APE file into MJ, so it writes the file info into its database. Un-APE the file into a waveform, edit it, save it, then re-APE it *to the original APE file*. Then, in the drop-down menu on the lower left corner of the file's MJ properties, change "Update Changed Files" to "Update All Files." then save the changes. This forces MJ to actually write the tag info back to your new file (which, since you un-APEd, edited, and re-APEd, doesn't have a tag any more).
Hope this helps,
Bill