The only tuning software for a C6 is LS2edit and its only for the 2005 and will not work on a 2006. It also looks like it does not support the TCM controller for the auto trannie so I would not be sure that all could be done in tuning when adding a SC'er
Better chances if the car is a '05 and using manual trannie.

In any case, the bottom end still is a weak link and I just saw another car with a maggie SC'er blow a head gasket and took out 2 pistons so anytime you add boost to a stock Corvette engine the chances are high that engine damage will occur long term though chances are better if just adding the SC'er, larger injectors, and very custom tune and NOT adding other mods such as radical cams.

Keep in mind the LS2 has even higher engine compression then what the LS1 has so the higher compression is the better chances of internal engine damage so if really wanting to be safe with a stock bottom end is to reduce the compression