This huge Act follows from the MoD Strategic Defence Review 1998. The Review put what in military jargon is hideously referred to as "jointery" at "the centre of the defence planning process" (see para 15 of the official explanatory notes to the Armed Forces Act 2006 available on the Parliament website).
Apart from a few sections which came into force on Royal Assent on 8th November 2006, the main Act comes into force on a day or days to be appointed by the Secretary of State (see Armed Forces Act 2006 s.383). The Armed Forces Act 2006 (Commencement No. 1) Order 2007, SI 2007/1442 brought into force on 4th June 2007 the important changes noted below which replace the one-off courts martial that must currently be convened for each trial. The bulk of ther Act was in force by 31st October 2009 (see Armed Forces Act 2006 (Commencement No. 5) Order 2009, SI 2009/1167).
One of the most important purposes of the Armed Forces Act 2006 is to establish a single permanent Court Martial, covering all three Services, to replace the one-off courts martial that have previously had to be convened for each trial. The intention is that there should be "a single, harmonised system governing all members of the armed forces" (see para 16 of the explanatory notes to the 2006 Act (pdf version)).
The Legal Services Commission (tel 08457-500640) has been charged with responsibility for locating an appropriate duty solicitor to represent members of the armed forces who wish to be represented at a new style military custody hearing and who have not nominated a solicitor or who do not wish to use the services's in-house legal department.
There is a complete section on the Ministry of Defence website re the Armes Forces Act 2006 which includes links to a new (October 2009) Manual of Service Law vol 1 & 2 and Manual of Service Law vol 3 and an official overview of the Service justice system and Armed Forces Act 2006.