I will be recording and editing 16 tracks using CEP under Windows 98SE. I then want to transfer the files to another engineer who uses protools on a Mac.
Can I just save the files as .AIF files, burn a data CDROM and give it to him, expecting everything will be fine?
Yes, so long as you're not trying to preserve any mix data. I presume you're just passing along files. This will work if they are perfectly continuous files and if they all start at the same point in time, or for which you have sync / offset data to the sample.
Actually, ProTools can open Wav files, I believe, so the conversion may be unnecessary.