Leah Farrell has written a short article on AQ command; key points:
Key Points

1. Al-Qaeda’s decentralised operating structure has cushioned it from the impact of droneattacks and arrests. A clear hierarchy remains intact, supported by robust and adaptable command and control processes, despite the losses it has suffered since 2001.

2. This modus operandi for external operations plots has remained remarkably constant in recent years, with plot members assigned several points of contact who provide technical and logistical support.

3. Nearly all recent disruptions to Al-Qaeda’s operational activity have occurred outside of its Pakistan-based command structure via the arrest of couriers tasked with facilitating franchise communication or co-ordinating the
activities of operatives in the West planning for attacks.
Full article:http://allthingsct.files.wordpress.c...20-command.pdf

One caveat… I wrote this in September/October last year so it is a little dated in terms of drone attacks etc. However, I still stand by the arguments I made in this piece.