Do you mean you are installing a higher stall converter?
The main thing this will mess with is how your torque management works. You will probably want to disable it and let the converter absorb all of the torque on the shift which will soften things up a bit.
Now you say SCT has more options, but you are referring to the PRP software from them. This is equivalent to the Commando package from Sniper. That package is priced to compete with it and has the same or more features as the PRP software.