All you have to do is the following
a) install the JDE as per instructions
b) put the .JAR/.JAD files in a directory
c) Run RAPC.exe (comes with Blackberry JDE)
"rapc import="c:\Program Files\Research in Motion\Blackberry JDE 3.7\lib\net_rim_api.jar" codename=<FILENAME> -midlet jad=<FILENAME>.jad <FILENAME>.jar "
d) Upload the .COD using javaloader

If you can upload the COD using javaloder you should have no troubles getting RAPC to work. I created a batch file (.bat) for this purpose...

If you upload it to your Blackberry and do not see the Icon on your ribbon, you have done something wrong. A successful upload will show an app on the ribbon..