IDW Publishing publish a series of Transformers comics that are set in the Michael Bay universe and explain more into the universe that the movies couldn't explain. I read them and enjoyed them and helped me get a better understand of everything that's going on. You can find the TPB books at like Borders, B. Dalton's, or even iTunes, but if you want access now, you can watch them on YouTube.
Transformers Movie Prequel:
Chapter 1-http://www.youtube.com/watch?v=tJnCjo-LUCM (http://www.youtube.com/watch?v=tJnCjo-LUCM)
Chapter 2-http://www.youtube.com/watch?v=qQQKmqwuLXQ (http://www.youtube.com/watch?v=qQQKmqwuLXQ)
Chapter 3-http://www.youtube.com/watch?v=Aaj3RK4v1W8 (http://www.youtube.com/watch?v=Aaj3RK4v1W8)
Chapter 4-http://www.youtube.com/watch?v=toYrv4G6wFg (http://www.youtube.com/watch?v=toYrv4G6wFg)
The Reign of Starscream (Takes place after first movie):
Chapter 1-http://www.youtube.com/watch?v=NBa43QLo54A (http://www.youtube.com/watch?v=NBa43QLo54A)
Chapter 2-http://www.youtube.com/watch?v=U-bZiFv4SEw (http://www.youtube.com/watch?v=U-bZiFv4SEw)
Chapter 3-http://www.youtube.com/watch?v=ytouCCyecMc (http://www.youtube.com/watch?v=ytouCCyecMc)
Chapter 4-http://www.youtube.com/watch?v=UE09S1kWbuw (http://www.youtube.com/watch?v=UE09S1kWbuw)
Chapter 5-http://www.youtube.com/watch?v=It-bL7U8J0U (http://www.youtube.com/watch?v=It-bL7U8J0U)
Transformers: Revenge of the Fallen Prequel: Alliance (Takes place after the first movie and The Reign of Starscream, leading right up to Revenge of the Fallen):
Chapter 1-http://www.youtube.com/watch?v=2yZs8_svTnY (http://www.youtube.com/watch?v=2yZs8_svTnY)
Chapter 2-http://www.youtube.com/watch?v=HsRn7zSoS0c (http://www.youtube.com/watch?v=HsRn7zSoS0c)
Chapter 3-http://www.youtube.com/watch?v=OL3mYFA1n18 (http://www.youtube.com/watch?v=OL3mYFA1n18)
Chapter 4-http://www.youtube.com/watch?v=8F-55r4QtcU (http://www.youtube.com/watch?v=8F-55r4QtcU)
Transformers: Revenge of the Fallen Prequel: Defiance (Explains how Megatron became evil and how the war began):
Chapter 1-http://www.youtube.com/watch?v=tJnCjo-LUCM (http://www.youtube.com/watch?v=tJnCjo-LUCM)
Chapter 2-http://www.youtube.com/watch?v=QEzYqG7CJHY (http://www.youtube.com/watch?v=QEzYqG7CJHY)
Chapter 3-http://www.youtube.com/watch?v=ieBf8HR6VMM (http://www.youtube.com/watch?v=ieBf8HR6VMM)
Chapter 4-http://www.youtube.com/watch?v=SOYKvsAFEM4 (http://www.youtube.com/watch?v=SOYKvsAFEM4)