www.makemkv.com

Im not fully understanding this.

I am using make MKV to backup my blue ray disk and handbrake to compress is. in makemkv i am selecting all the subtitles and forced subtitles. Where my problem is i don't understand what I need to select in handbrake. I have tried several different options and i cannot get subtitles. I am using plex to play my movies and when i go to change the subtitles nothing is listed.

Hopefully someone can tell me what I'm doing wrong

Far too many variables to say "do this and it will work".

First thing, though, is to make sure you're running a current version of handbrake; they're up to 0.10.5 as a release version, and there is about a year's worth of improvements over the release tied up in the nightly builds. Versions prior to 0.10 did not do much with Bluray subtitles.

Next, read through this on their site: https://forum.handbrake.fr/viewtopic.php?f=11&t=16527

If you're still having problems, read https://forum.handbrake.fr/viewtopic.php?f=6&t=31236 and post a message in the appropriate forum for your version of handbrake (Windows, Mac, Unix) with the activity log. They even have a template when you click on "New Topic" to make sure you cover the stuff they need to give answers.