Last week I upgraded from BizTalk 2006 CTP build to Beta 2. It went smooth thanks to upgrade paths supported by BizTalk installer. Although I did backup BizTalk databases I did not have to use them after installation - all artifacts loaded fine. The installation process itself is painless and easy (big improvement over BTS 2004) but make sure to read latest installation guide http://go.microsoft.com/fwlink/?LinkId=46922 which is pretty thorough.