Remote Buddy will control the latest generation of Plex that it finds while Remote Buddy launches.

For added clarity, here are a few scenarios:

1) If you have Plex and Plex/HT installed, it will control Plex/HT. 
2) If you have Plex installed, it will control Plex. 
3) If you have Plex installed, launch Remote Buddy and then install Plex/HT, Remote Buddy will control Plex. You need to relaunch Remote Buddy to control Plex/HT. 
4) If you have Plex/HT installed, launch Remote Buddy and then install Plex, Remote Buddy will control Plex/HT. You'd need to remove Plex and relaunch Remote Buddy to control Plex/HT.

Best regards, 
Felix Schwarz