Take the freaking thing down the road and see if the speedometer is off. If it is, plug in your tuner and change it in the command prompt. If it isn't...then its built into the tune.
The SCT tuner does not read the current program in the computer. It simply changes the values of what ever parameters are in the computer. So, if you are running a stock tune....and you tell the handheld that you want to advance timing +2 degrees...it will add +2 degrees on top of the fuel trim tables in the computer. If you are running an aftermarket tune. and you tell the handheld to advance +2 degrees. It will add this to the fuel trim tables in the computer that are already bumped...this can really jack sh*t up.
Now, on the flip side with gears. I think it is simply replacing the values in the computer. not building on them...(its all just math) for gears and tire revolutions. So, I think...and I repeat...I think. It simply replaces the value in that sector for the speed sensor. However, when you plug in the handheld....its not going to say you already have a setup for a 4.10 or 3.73 or stock. Its simply going to ask tire revolutions and gear size you want to plug in.
Now, here is catch 22. If the tuner checked the box that says the user has the ability to change variables in the tune before he saved the tune file. You will be able to select the tune file for reload and it will allow you the option to change parameters before uploading. If he did not do this and you plug your handheld in to adjust the gear ratio and you just select a different tune. You will over ride the custom tune file with the canned tune file. This will change the gear ratio for sure..but it will also start adding variables to some of the parameters that the costume tune file changed instead of completely replacing the costume tune file stuff with stock variables then turning around and adding the new variables to the stock variables....Sh*t can get really F*cked up doing that.
Best rule of thumb when uploading tunes.....Re-turn to stock. Then up load new tune...becasue, depending on what has been written in the tune file to change in the computer...will determine if its a replacement value or a mathematical value that uses what ever number is in that particular sector as the variable for the mathematical formula.