I have a bunch of MKV movies that I'm converting to MP4/M4V using MKVTools to play on my AppleTV. However, the final MP4 is just one long file. Is there any way for me to add chapters to the file so I can jump ahead when watching on my ATV2 instead of rewinding the whole way? Thanks.
I'm not familiar with MKVTools, so I don't know if there is a way using that. However, you can create chapters and add titles with MetaX. As long as you know the length and title of each chapter (most listings are found easily with a Google search), you can sub-divide the movie into its correct segments. If you have a TagChimp ID, MetaX often finds and adds the chapters and titles without the need for you to transcribe the information.
FYI, I did this just last night where my rip of Dr. Strangelove had over 40 chapter breaks whereas the movie has 28. Allmovie.com had the chapter times and titles, so I used MetaX to eliminate the old chapters, and then I added the correct timings and titles. A couple are off by a second or two (due to errors in the information, not the software), but it's all close enough that I'm not going to try to fix it.
I believe Subler has this capability too, but I use MetaX for chapters so I have no idea how it works.