I had to search for the answer, but here's what I do (both of my computers with AA/CEP loaded on have been set loooooooonnnnnng ago to a single file type).
I finally discovered that I save as Windows PCM (*wav). One reason I do so is for maximum compatibility (as I understand it) between softwares. Another reason is that they are uncompressed, and I'm a firm believer in recording and saving everything with no data compression. If you must generate an mp3, do that at the end of the process, after you've saved the .wav version.
Other people think you can lose data without losing the impact of the music, but in my opinion, using mp3 compression is the equivalent of taking pristine uncompressed digital audio and turning it into low-fi cassettes. I have heard people rant about there being no audible difference, but I can sure as hell hear it. Consumers (and some musicians) mistake convenience for quality.
But those crappy-sounding mp3s are not restorable to the original. Storage space keeps going up and up, and it's just one more thing to regularly update. For example, my recording computer started out with 20GB, and over the years has evolved into 40+400 internal drives, with another 500GB or so of external drives.
The day of the mp3 is numbered: before very long there'll be so much storage space everywhere that mp3 compression will be unnecessary. Why do something harmful and irreversible at the beginning?