So I recently purchased an Asus bluray reader (and writer) with the intent of ripping some of my critical blurays to a 4TB Seagate drive that I have connected to my Netgear R7000 USB port (poor man's NAS for now).
I want to be able to watch the blurays from devices within my house (Pivos XBMC player, HTPC with XBMC). Retaining the lossless audio and video is pretty paramount for me as I've invested considerably in my video/audio system.
I've tried to read online and it appears there are tons of "recommended" routes. MakeMKV. MakeMKV followed by Handbrake (possibly to reduce the file I assume?). AnyDVD. ClownBD, etc. etc.
I've been experimenting thus far with just MakeMKV as well as then taking the MKV file and encoding it using Handbrake into a M4V file and decided to try the film I am Legend. This quickly started to get confusing. E.g., ignoring the multitude of video options (I just left it at 1080p and 20 as the default to try it out) the audio then became that much more confusing. Do I select AAC Passthrough, DTS-HD with AAC passthrough, etc. Ultimately I tried AAC Passthrough and when I played the bluray via my Pivos box I could only get Dolby Digital from my Processor (Integra DHC-80.3) when I wanted to retain the original DTS-HD recording so clearly chose the wrong one. Video looked pretty good, though I started wondering if it was a bit soft. So I then simply copied the original 15GB .mkv file that MakeMKV created, and tried playing that but it was just constantly stuttering in the Pivos Box (wondering if this is hardware related as it doesn't stutter on my laptop).
I then read up some more, and came away more confused about whether to keep an ISO file (and possibly use some sort of external player in XBMC?), keep the mkv container, etc etc.
In any event, before I keep ripping along, is there a recommended way to preserve the video and lossless audio of the bluray?
Is AnyDVD that much better than say MakeMKV and/or Handbrake? The cost really doesn't bother me if it is. I'm just looking to be able to rip blurays in a fashion where 1 or 2 years from now I say to myself "crud, I should have done it this way instead as I'm losing video and/or audio quality". It takes hours to rip a bluray (I'm using a ~2010/2011 Arrandale i7-640 based laptop for this at the moment), so ideally just doing it right the first time is of obvious importance! 
Or is this whole post just nonsense as there is no "right" way of doing it?