Please point me to an explanation that I may have missed.
I'm a techie but a major noob when it comes to ripping blu-rays, so please be gentle

I have "Avatar (Extended Collector's Edition)" 3-disc blu-ray that I bought in late 2010. As many of you know, disc 1 includes 3 cuts of the first movie. I also see three large title files on the disc. I am aware that sometimes, with multiple cuts, scenes are spread across multiple files and shared between versions. I also see a "segment map" which I think is related to this.
Is there a generally applicable procedure to rip a specific version? I'm sure Avatar will not be the only one I will encounter like this. In this particular case, I'm interested in the extended collector's version. However the runtime of the longest track is a little less than 3 hours while, from what I read, this version should have a runtime of about 3 hours 15 mins.
I'd appreciate some guidance.