I'm no expert but here's what I've read many times. If you're just doing the pipes and not a higher flowing airbox, bike should be able to adjust fine on its own. However, bike was factory lean to begin with and it will be leaner after doing this. Dealer can download new software to compensate for the pipes but it only returns it to the original, factory lean condition. Very small additional expense after doing the pipes to do a TFI fuel tuner and different airbox and now you have control of the AFR and have finished your Stage One.
I'm sure the pros on here will point out any errors I made unless I got extremely lucky and got it right the first time!