In the mythbuntu control center, you configure this combination by selecting the "Windows Media Center Transceivers/Remotes" (MCEUSB2 in <mythbuntu 9.10) setting in the drop down list. It's that easy.
I didn't like the default key mappings for mythtv, so I edited ~/.lirc/mythtv until I had each button configured to a unique keypress. I then modified the key bindings for the frontend in mythweb until each button operated the way I wanted it to.
After a while I got my hands on the harmony 550 remote. During the programing of the harmony remote, I just selected "Windows media center remote" as the device I was controlling. The harmony remote sends the same IR commands as the AVS remote it replaced. I did tweak the logitech settings so that my LCD screen has buttons for "Recordings", "Music", "Videos", etc. and those mapped to the buttons at the top of the AVS remote.