The way I did the upgrade was:
Deactivate Media Composer
Uninstall Media Composer
Upgrade/Install Lion
Install Media Composer
My first attempt was to just do an upgrade. Media Composer 5.5 appeared to be working fine, but I wanted to install version MC6. After some testing I decided it is better for me to run MC6 on Lion in its own partition (the partition runs only Lion and MC6, and soon BCC8). I have had all sorts of difficulties trying to get BCC 7 to work on MC6 with Lion. Ran into some difficulties in uninstalling BCC7 in Lion, Made periodic backups after successful steps.