This is tricky because the MP3 format doesn't support exact seeking. That means you can't close / reopen the file even when switching tracks.
Some more thoughts...
I'm not sure how winamp does it, but you can jump to a certain postion in a track by entering its time etc. If i have other files in addition to the big audio file in the playlist, winamp manages to jump to them sans problem. i can go back to the big one, and mp3cue displays stuff as normal. Does this address what you meant above ?
Is it possible to access an mp3 by converting from time to frames. If you know how long a track is then is there a way to calculate a frame offset for it ?
Mp3cue plugin for winamp, only opens the file once when its selected for play. When the track changes its only the track name display that updates. The file is still playing as is. So to support CUE files would require the playing now file list to update or the track list when the album is clicked on.
i would imagine that during import, if MC detects a cue file it would associate it with the big audio file, in a similar way that cover art images can be associated to a media file. To keep it simple, the cue filename needs to be the same as the audio file. This is the way mp3cue works.
I imagine a structure holding the track data ( got form the cue file), associated with the big audio file stored in the library.
I am undecided on whether its better to store stuff in the library or use an intermediate stage like you have for APL files. On one hand any modifcations are done on the intermediate step ie the APL file, leaving the cue file unmodified. I thought of skipping the APL stage and going directly into the library.
Now that i think of it, its a tricky problem, but not impossible. Would defnitely set MC apart from the rest.