Just install the extesions the same way you would for VS 2005. As for the toolkit, if you create and application that uses the 2.0 framework and add the toolkit to the toolbar you will ONLY see the tool available in 2.0. The 3.5 AJAX Toolkit controls won't even show up for a 2.0 application.
I have both running successfully and have had no compiling problems.
"Hokey religions and ancient weapons are no match for a good blaster at your side."