Custom TCM Initial Setup

I will be installing a Hemituner custom TCM later today. Once installed, I will need to take a new backup and reload my custom tune from the Trinity, since it has to be placed back to stock before the install. What I am unsure about is how to setup the quick adjust menu in the tuner. In my Trinity, I currently have the gear ratio changed to 3.55, the rev limiter at 6700 and the *Raised Shift Points* option. I am not sure whether or not to reselect these options in the tuner since the TCM itself is programmed for the 3.55 gears, a 6800 shift point etc..

Thanks for any advice.