I noticed in plex iOS it has an icon for chapters. When I ripped all my movies I was not aware plex could show that information. Is there anyway to add chapter markers and chapter titles without re-rendering everything?
What do you mean by “rendering”? Recompression?
No. At least for mkv files you only need to “mux” the chapters in. I did this for my concert DVD rips. I extracted the chapters, edited them with MKVtoolnixGUI (I put in proper names to quickly find particular songs) and muxed them back in (again with MKVtoolnixGUI.)
There may be something in existence for mp4 files too, but I haven’t researched that yet.
(edit: you might wanna look at this http://www.tweaking4all.com/home-theatre/adding-movie-information-metadata-to-mp4-m4v/ )
Besides, since almost a year Plex server fetches chapter information from an online source if you match a movie with the default metadata agents.
You can verify this by calling up the mediainfo XML of a movie.
then go into the address bar of the browser window and edit the part of the URL which reads includeExtras=1 to read includeChapters=1, hit Enter
at the end you should see a list of chapters, (if available for that movie)
it will look like this if the chapters are ‘named’:
<Chapter id="32720" tag="Babysnakes Rehearsal" index="1" startTimeOffset="80" endTimeOffset="132080" thumb="/library/media/144309/chapterImages/1"/>
<Chapter id="32721" tag="This is the Show They Never see" index="2" startTimeOffset="132080" endTimeOffset="484400" thumb="/library/media/144309/chapterImages/2"/>
<Chapter id="32722" tag="Baby Snakes" index="3" startTimeOffset="484400" endTimeOffset="609680" thumb="/library/media/144309/chapterImages/3"/>
<Chapter id="32723" tag="Bruce Bickford/Disco Outfreakage" index="4" startTimeOffset="609680" endTimeOffset="985520" thumb="/library/media/144309/chapterImages/4"/>
<Chapter id="32724" tag="The Poodle Lecture" index="5" startTimeOffset="985520" endTimeOffset="1288400" thumb="/library/media/144309/chapterImages/5"/>
without names, the chapters will miss the tag=...
Once you put the video file with chapters into Plex, you may need to re-analyze the file.
As with all embedded metatags, your Local Media Assets agent must be active. (It is never a good idea to deactivate it completely. If you often have to deal with wrong or spammy metatags, just drag the LMA agent downwards, so the online metadata sources take precedence.)
Regarding m4 files: If you are happy to use you MacBook then also the application Subler is your friend. If allows you to search for the chapter information on the internet and then to add these as text stream to your mp4 files. Plex will then import that information when it re-analyses the file.
Hint: Do an extra “optimize” run at the end.
Oh sweet thank you both for the information! Yes I did mean having to compress the file again.
For MKV files, you don’t even need to remux the file. You can just use mkvpropedit to add chapters from a chapter file, such as ones found at ChapterDB. Instead of possibly minutes, it takes around 1 second. 
Here’s an example:
mkvpropedit "The Avengers (2012).mkv" --chapters "The Avengers.chapters.txt"
