New and need advice

I'm new to this forum and have been reading around and i have lots of questions. First of all I have an iMac, 2 Macmini's and about 200 blue rays with a 2113 Denon AVR (accepts hd audio). I plan on ripping to blue rays from the iMac to a server which I have yet to build.

I would like the server to use flexraid or unraid and MySQL. I've read the threads about raid software but my head just spins around and around. Can anybody put it in layman terms and clear it up? Haha. Also want to use 3tb hard drives, not sure if they support that.

As far as ripping the blue rays I plan on using anydvd hd. I want uncompressed audio and video with forced subtitles and chapter information. Don't need any of the extra stuff beyond that. Will anydvd hd work for this? Also should I leave it in iso or put it in mkv format? I need it to be future proof.

For the Mac minis. One has the intel hd4000 the other hd3000. From what I understand I need to run windows on these to get hd audio out? If that's the case should I run windows 7 or 8? Also, is it better to stick with the tried and true Eden or jump right into frodo?

Thanks for any advice you can give! I feel like I'll have a steep learning curve ahead of me but I'm ready for it!