power commander question

[05yamahafz6]

Getting ready to install the power commander i just purchased to go with the two brothers exhaust and k&n filter. Can someone tell me, does it matter if I do a throttle body sync with the power commander connected or should you always disconnect the power commander to do a throttle sync.

 

[Phrozen]

Sync your throttle bodies with the PC3 connected, make sure you calibrate your throttle (TPS) in the dynojet software.