1. I don't think it makes a bit of difference. I guess the easiest way would be to rip right to AIFF using one of the Apple friendly programs. Like you, I've done both: rip to FLAC using EAC then converting to AIFF. Now, I simply use MAX to rip right to AIFF. I've noticed no difference in sound quality.
2. I don't think this process is perfect. I remember when I converted FLAC to AIFF, I had to fix quite a few things in Itunes.
3. According to some, the Itunes ripper is not as good as MAX, so I would recommend using just MAX. For the most part, Apple does a nice job keeping tags and clearly ID'ing files once there in your music library. Yet, you may have to change the name of the actually file or just within Itunes.
I'm pretty anal, so I spent quite a few hours going over my Itunes music library to make sure everything is labeled correctly. I suggest you continue to experiment and find your way.
