I've been working with BizTalk 2006 and Visual Studio 2005 daily for the last few months and have to say I am severely disappointed. The UI crashes at least a few times a day, and there are a number of gotchyas that can really steal a LOT of time from you.
One such gotchya is related to the BizTalk mapper. It seems that if you add any type of project to your solution that is not a BizTalk type, you run the risk of breaking your mapper. Not that VS tells you this. You get a cryptic message saying 'Failed to load source schema'. Luckily there is a newsgroup thread somewhere out there that has some relevant discussion on this.
If you are building a BizTalk solution, I recommend you keep all your other types of projects (Database, C#, Reports, etc) in another solution.
I'm hoping that the Visual Studio service pack will solve some of these issues, but only time will tell.