Re: audio, most Blu-ray remotes have an AUDIO button that lets you switch between audio sources. The default 5.1 track mixed down to stereo would get a little muddied, so it’s safest to recommend one of the stereo tracks for best clarity. Some players don’t understand DTS-MA under some/all circumstances, so won’t play the default track (either silence or they’ll pick another track).

Re: subtitles, Project Threepio has a huge, detailed README that should answer all questions. PM me if you need a link to the complete project. In short, the best thing to do is to unpack the contents of the ISO, and make a new ISO with subs embedded.