thanks for asking.

The setup is pretty simple. If you have a programmable remote (a 
universal remote is usually something different as it doesn't support 
actual programming as far as I understand it) and an Apple Remote:

1) Enable support for multiple remotes in Remote Buddy and create as 
many logical remotes as you need to reach your desired, total button 
count (desired button count / 6 = number of logical remotes needed).

2) Program your universal remote with recordings of all buttons on 
your Apple Remote. Also point the remote to your Mac and press the 
Menu button twice, so Remote Buddy knows about that remote. Choose a 
different logical remote control for every ID.

3) Then, on the Apple Remote, press Play and Menu together for a few 
seconds. This will change the internal ID of the remote.

4) Repeat 2) + 3) as often as needed.

5) Repeat this as often as necessary to get the number of button 
codes you want to use.

6) Assign the recorded codes to buttons on your remote. Then, in 
Remote Buddy, assign the functions you want to use to the different 
logical remotes as you would for different real remotes.

Hope that helps.

Best regards, 
Felix