Hmm I've fiddled around with OBS and I remember it being hard to wrap my head around. But I was using it to live stream, not so much record footage. By the sounds of your experience with it, not the greatest program to begin with.
Unfortunately, I think with iMovie you're going to have a hell of time syncing sound. I think iMovie would work fine if you were working with the type of files FRAPS gives you. It's not impossible, but I would strongly suggest working with Premiere if you're going to record audio and video separately.
Oh man, screw FLV. I feel like you might be shooting yourself in the foot by adding another conversion step in the process. If you can find a way to record to .mov or .avi you'll be way better off.