How to add Chapters, Subtitles and convert for itunes?

[TC1006]

Hello,
I am have been reading a quite a bit of posts trying to find out what would be the best way to convert a blu-ray movie to a final destination in itunes in a 720P format with chapters and subtitles.

Here is what i've been able to do.

Rip movie to Hard drive via ANY-DVD.
Mux via TsMuxer and remove unwanted tracks and other subs and create a m2ts file.

But this is where i get stuck, i have opened the file in Handbrake to encode for itunes, but the chapters information is missing and so are the subtitles. Are there better softwares out there to achieve this?

Could someone please tell me what would be the best way to incorporate chapters and subtitles and then encoding into H264.

Thanks.

[TC1006]

So i am able to get a little further, here is what i am able to do:

Rip to HD using AnyDVD
Use RipBot to Demux and Encode with Subtitles.

However, i am still unable to get the chapters added on there. I have tried various things but still no luck. Can anyone please explain how to get the chapters added to these files? Thanks