If there is an up to date proper plugin installation explanation for Bukkit/Spigot type plugins floating around, I don’t know where it is. (And I apologize for essentially reposting this!) There is fragmented and incorrect information floating around, and it made it fairly difficult for me to figure out where the server files are located and what to do with the plugins I have downloaded. So, out of frustration, I am posting this to help anyone else that might be having the same issue.
**Disclaimer: Some Plugins might require more steps than this, but the vast majority of plugins are installed as explained below!
To access your server and transfer files around you will need an SSH/SFTP client. One of the many places I looked searching for this information mentioned WinSCP, so that is what I am using. It can be found Here.
Using Win SCP is easy and is outside the scope of this guide. The most important thing is you want to use the username root (for full access. You should be able to actually install plugins using the mc username as well, since mc actually owns the directory in question, but I just used root to be safe) and the password that you set up when installing MineOS Turnkey to log into the server.
If you check the server console’s main menu, there is a line that lists the username IP and port you should connect to using this client. Something like SSH/SFTP: root@192.168.x.x (port 22). That is all the info you need to access the server files. (Other than your password)
Now comes the part that I actually had trouble figuring out. LOCATING the proper directory. If you are googling this information you will find people pointing you all over the place. I don’t know what those people did to install their servers in those locations. (I don’t recall picking, pretty sure MineOS just did it for me, if I did have a choice though, I just picked the default directory)
That directory is:
/var/games/minecraft/servers/(servername)/plugins
^That is where your plugins folder SHOULD be located!
**It has been pointed out that you might have to manually add the plugins folder after the (servername) directory, although in my case I didn’t have to! 
All you have to do now is use your SSH/SFTP client to transfer the ,jar files associated with the plugin you are installing into that directory.
**Note: Do NOT extract the .jar and put those files in there, it won’t work! WorldEdit, for example, said to download and extract the .jar file into the plugin directory, but when I downloaded it from their link, it downloaded as a .jar. I’m quite sure they expected it to be a .zip file instead and wanted me to extract the .jar from the zip, but the wording they used could go either way and led to some initial confusion on my part. So for clarification, you want the .jar in that directory, not the contents of the .jar!
**Update: Watching Will’s video, I noticed something I hadn’t before. In the bottom right corner of the WebUI there is a place where you can delete files from your server. This actually lists the path for your server as well, so if it is somehow installed in another location, you could check there to find it! 
That is it people. Reboot your server, and assuming the plugin you elected to install is compatible and functional, minecraft will do the rest!
Hopefully this is helpful to someone, and I’m sure it has been thoroughly explained somewhere before, but that explanation somehow did not present itself to me while searching around the interwebs! Maybe this one will be a little easier for people to find.
Cheers!
