Yes you can use a Harmony Remote to have more than 6 keys.

In Logitech Database, there is a device name "Plex Player" (Multimedia computer/Plex) which was defined to control Plex. You can use this device to setup your Remote then have it known to Remote Buddy.

That's what i am doing on my MacMini HTPC (still work in progress). If you go to hardware tab in RB preference window, you have to check "enable support for multiple ..." then "Automatically authorize..". From the harmony remote just press a key and RB will discover ids (a number from 150 to 160).

To help identify which keys are corresponding to each remote, you may have to name Remotes to something meaningfull. Here is a list I grab from Plex forum :

Harmony button - RemoteID + Button 


OK - 150 Play/Pause  
Up - 150 Plus 
 
Down - 150 Minus  

Left - 150 Left  

Right - 150 Right

VolUp - 152 Plus 
 
VolDn - 152 Minus 


ChUp - 158 Plus  

ChDown - 158 Minus 


Mute - 152 Play/Pause 
Prev - 153 Minus 
Menu - 150 Menu  

Exit - 155 Plus  

Guide - 157 Play  

Info - 153 Plus

Stop - 151 Play  

Replay - 160 Plus  

Skip - 160 Minus  

Play - 151 Menu  

Rec - 155 Minus  

Rew - 154 Plus  

Fwd -154 Minus  

Pause - 152 Menu

1 - 151 Plus  

2 - 151 Minus  

3 - 151 Left  

4 - 151 Right  

5 - 152 Left  

6 - 152 Right  

7 - 153 Left  

8 - 153 Right  

9 - 154 Left  

0 - 154 Right  

Clear - 154 Play  

Enter - 153 Menu

Blue - 159 Menu  

Red - 159 Left  

Green - 159 Right  

Yellow - 159 Play

Aspect - 157 Plus 
LargeUp - 159 Plus  

LargeDown - 159 Minus 
PwrToggle - 157 Menu  

Queue - 157 Minus  

Sleep - 154 Menu

F1 - 155 Left  

F2 - 155 Right  

F3 - 155 Play  

F4 - 155 Menu  

F5 - 160 Left  

F6 - 160 Right  

F7 - 160 Play  

F8 - 160 Menu  

F9 - 158 Left  

F10 - 158 Right  

F11 - 158 Play  

F12 - 158 Menu  

F13 - 157 Left  

F14 - 157 Right

Regards 
Patrick.