Moved to ePO for better handling, someone should answer you soon.
The compatibility tool is run on an existing server to make a determination if you can safely migrate from your existing epo server version to 5.x.
I dont think that was your real question though. You sound like you want to port your dbase to another new epo server. Before we walk down the anticipated road here are a few questions first?
1. What products do you currently have deployed?
2. How many systems (nodes) do you manage?
3. Do you have any repositories?
Your other question sounded like you wanted to back up your policies. Goto the policy catalog and backup all policies for all products And dont forget mcafee agent policy too.
Depending on your answers may be either straight forward or be more complicated. We will cross that bridge at that time.