You have two choices with EFI, you can purchase either a V2 or autocal. The difference between the two is with the V2 you have the ability to write your own tunes or purchase tunes from any tuner you choose. The autocal is cheaper but is linked to a particular tuner. The function of both is similar in that you can datalog and check & clear trouble codes and such, may be more the V2 can do but I went with an autocal so I'm not too familiar with it.
Basically you will get the device and read out the trucks stock file and send it to the tuner you choose with what hard parts you have on the truck and what your looking for performance wise. They will then write a tune or number of tunes(tow,street,race,etc.) and email them to you and you install it to the device then load it on your truck like you would any other programmer. You run it see how you like it, maybe datalog a bit and if you need changes you can send your tuner the data logs and they can adjust. It really is the only way to go for 06-09 trucks.
Hope this helps