I wrote a post some time ago back in October 2015 on how to run a Minecraft server on Debian 8. You may find this useful? It is rather old now so I'm not completely sure how relevant it still is.
You're looking for something like screen to keep the SSH session persistent. Context on these two commands below is given in the above link.
- sudo apt-get install screen
- screen ./run-minecraft-server.sh
There are other choices outside of screen but this should suffice.
Using screen is great. On top of that, I'd also set it up so it starts on boot. Even if you use screen, if the server is shut down or rebooted, you'll still need to enable the server again. Not really a boot script, but I added a screen command to my rc.local so it executes after boot. More details here