Howdy,

I have the Oblivion and Skyrim soundtracks on CD and I've ripped them to .FLAC files.

What I'd like to do is add these to Morrowind. Is this just a matter of converting to MP3 and then dropping them in the correct folders?

I think so. In Morrowind there's just Explore and Battle folders and I've been able to drop pretty much whatever I fancy into one of those two. So, yeah, convert to MP3 and you should be good.