There's a slightly surprising dearth of good history of the CIA in general, partly because it's a relatively young intelligence agency, but also because the Agency is very cagey about its archives. And, unfortunately, there's also an awful lot of bullshit written about the CIA (and all espionage agencies.) The best single text I can suggest is Legacy of Ashes, a very good — and very critical — history of the first 60 years of the CIA written by Tim Weiner.

There's plenty to read in there about the Agency's paramilitary operations over the years. There's also some great investigative reporting being done around the post-9/11 paramilitary character of the Agency, but that's outside the 20-year-rule for this sub.

It's worth noting, though, that the CIA (like all government departments) is prone to regular internal reorganisations and renaming, so the 'Special Activities Division' tag may not be canonical nomenclature throughout the Agency's history. For example, the Directorate of Plans becomes the Directorate of Operations becomes the National Clandestine Service, and so on. It may not even be that department's name now; it's just the one that has embedded itself into the public/media lexicon.

"Jawbreaker" by Gary Bernsten is a book written after the initial CIA incursion into Afghanistan following 9/11. The CIA censors had a fun time with that book cause good chunks have been redacted but Bernstein left them in there. It should be noted that Bernsten was a CIA Officer in the SOG/SAD and was an on the ground leader both in Afghanistan and the bombings in Kenya.

Another one is "Kill Bin Laden' by Dalton Fury. He was the on ground Delta Commander who worked closely with the CIA and has some good mentions in his book about working with them.

"First In" by Gary Schoen is another I have a read. The slogan is "How Seven CIA Officers Opened the War on Terror in Afghanistan" and he talks about establishing the network used to coordinate the CIA effort prior to the initial American Military intervention.

Like k1990 said, there really isn't a plethora of information on the Special Activities Division especially in regards to an overall history however, I would recommend reading into the MAC-V-SOG(Studies and Observations Group) which was part of the SAD during the Vietnam war. They were responsible for reconnaissance missions inside Laos, Cambodia, and North Vietnam and consisted of members of the C.I.A., Army Special Forces, Navy Seal Teams, and indigenous mercenaries. They were also involved with the Phoenix Program which targeted the Viet-Cong network.

I would suggest reading, SOG: The secret wars of America's Commandos in Vietnam, this one of the more popular books on the subject covering individual missions as well as the overall organization's structure and logistics system. While this is only a section of the SAD's history, and not an overall history of the organization, I still think that it will offer you some answers to your questions.