When I have been asked to help people with their Beo5, I have usually learned the IR codes using my old and trusty HP iPaq 2210. I found a program called RemoteControl II, this program will learn the IR codes in Pronto format for your remote. Just install the Remote Controll II on your Windows CE device, and begin the learning progress.
You can find Remote Control II here.
I usually just create a PocketWord file for each Pronto code learned, and when I have documents for each command on the iPaq 2210, then I transfer all the files to my computer.
Then it's just a matter of creating the TPF file with the Pronto codes for each command, and import that TPF file into the App, and finally test the product.
You can read more about the TPF file with pronto codes here