Unfortunately you are not able to run both side by side; so I would suggest you run 2009 in a VM and test your 2010 project in that if you need downward compatibility.
Remember, BizTalk 2010 is the only version of BizTalk compatible with R2 version of the Microsoft Server 2008 and SQL 2008. Setup is still roughly the same.
I have not been able to find a post or get a true explanation on “reserved words” in BizTalk; however there are a few you should stay away from. I have personally tested these.
You should refrain from using “BTS” or “EDI” anywhere in your namespace to avoid namespace property look-up issues.
I will be posting more about this as I work through the public version of BizTalk 2010 on Oct. 1, 2010.