So you have 2 different installations of MT, then? W/ 2 separate 'db' directories?
It's just a matter of which mt-comments.cgi you link to, right? ie. for Blog A you would link to the mt-comments.cgi for Blog A, and for Blog B you would link to the mt-comments.cgi for Blog B. You will probably have to tweak the OpenComments JS function a bit; like you may have to create two different functions, OpenCommentsA and OpenCommentsB, each of which links to a different mt-comments.cgi script.
I may be missing something, though...