Letter Offers Insight to al Qaeda, Points to Role of the Brotherhood

"Today's Washington Post has a fascinating look into the Salafist jihadi movements. The internal letter from the al Qaeda leadership to Zarqawi from December 2005 was translated and provided by the Combating Terrorism Center at West Point and is available here.
The most interesting element is the dismay of the "core" al Qaeda leadership (bin Laden, Zawahiri et al) at the Zarqawi tactics of killing other Muslims, especially Sunnis, and the insistence on following a much broader overall political policy, rather than just attacking the enemy militarily."
CT Blog

I would like to add that according to my interpretations of pro Iraq resistance blog, they run that command and control through humanitarian NGO's operating out of Jordan and Syria.