There really is absolutely no quality difference between FLAC and APE files - they are both 100% lossless (which you can easily test by compressing, then un-compressing using either codec).
I always use Apple Lossless simply because I can 1) use it in Foobar2000 using the M4A plug-in, and 2) can easily put the files onto my iPod.
I use dbpoweramp which makes the task of converting between different lossless (or lossy MP3 or Ogg etc etc) formats a piece of cake.
The only way there is a sound difference between the two formats is if you use two different programs, and one - for example - has some EQ settings which are not 'flat' for example. Believe me, lossless means lossless ;)
Glad you are enjoying the music :)