I already have the 5.3 installed. However,..

[Shon]

THere are several ways to do it. but one of the key things to do is to change the displacement in the PCM from 5.3 to 6.0, this goes into many calculations for the Air and Fuel.
if stock motors then the tuner would probably just take the VE and MAF tables from a stock file and copy over or if they have tuned them successfully they would pull from that db and put in those changes.