You can create custom actions in Remote Buddy to achieve what you want to do.

For pausing EyeTV and launching Plex, you can use this AppleScript snippet:

tell application "EyeTV" to pause 
tell application "Plex" to activate

Similiarly, for quitting EyeTV and launching Plex:

tell application "EyeTV" to quit 
tell application "Plex" to activate

... and vice versa:

tell application "Plex" to quit 
tell application "EyeTV" to activate

Best regards, 
Felix Schwarz