I would convert the ape to flac format, there is zero quality loss. I use mplayer to play my flacs, admittedly from the command line. I'm assuming there's a gui frontend for mplayer (for audio files) on maemo, I just haven't bothered finding it yet. Mplayer also has a 10-band eq, which can be handy.

Alternatively, you could convert to ogg format with some small quality loss, and use the default media player, with ogg-support installed..

There are also tools for splitting your large audio file into separate tracks using the cue file for split points. Google's your friend...