I know I could convert to MP3 when I needed to but most people strongly advise against transcoding files from one format to another due to a loss in quality.
Well that's the beauty of using APE. There is no loss in quality (in the sense that you are talking about) when you transcode from APE to any other format.
Think of it this way. Your PC can only play back WAV files. When MC (or any other media player) encounters an MP3, it has to decode that MP3 to WAV and then it can play it back. It's all seemless to you, but that's what's going on behind the scenes.
When you encode from CD to MP3, you lose quality, because MP3 is a lossy encoder. The same goes for WMA. So when the PC attempts playback of an MP3 or WMA file, it decodes it to WAV first. The resulting WAV file is inferior to the original WAV file that was generated from ripping the track from the CD.
So when you transcode from MP3 to WMA, the PC decodes the MP3 to WAV, then re-encodes that WAV to WMA. During the WAV -> WMA stage, you're starting out with an inferior WAV file, because it came from a quality-challenged MP3.
But APE is completely lossless. When the PC decompresses (not decode) the APE to WAV, it's exactly the same as the WAV you started out with when your first ripped the CD.
So if you transcode from APE to MP3, you'll get the same result that you would have had you gone straight from CD to MP3. In other words, no (extra) quality loss.