Comment recommending: Awesome WM (Score 1) 460
presuming you have some linux experience (else you might not find your way around it), awesome windows manager is a great solution and can definetely do what you want.
it features 9 "tags" - virtual desktops basically, but is completely configurable via a lua script. each monitor will automatically be controlled without difficult setup and it worked "out of the box" for me - except for the laborious install process;)