Currently there is no way to reprogram TimeFactor's onboard switches. They operate in 2 main modes- Bank Mode and Play Mode, (Looper is a third mode but is a part of Play Mode.)
Perhaps in a future release we could add a programming option for the onboard footswitches if enough people ask for it.
The FS1, FS2, and FS3 settings will make the Aux footswitches always operate in the opposite mode from the onboard footswitches. For example, if you set the T+R Aux switch to FS3, then the Tip+Ring Aux switch will do Bank Up when TimeFactor is in Play Mode, and Tap Tempo when TimeFactor is in Bank Mode.