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...
Yeah, APE is not the best for a mobile device. To much compression can be a band thing. FLAC seems to be more of a standard anyway (IMO, as I am not a audiophile).
Encode them to MP3 VBR or OGG Vorbis -q3. You'll save diskspace and you'll save battery life at the compromise of something which ~90% of the people are not able to distinguish in a blind test (on top notch equipment) as tested by C'T.