Actually, you can do either or both.
Ungawha has a GSXR 1000. Mind you this is a race/street bike, but the principles apply to both. He just had the front lowered 13mm (and then raised 5mm). Then the rear was raised almost a half inch. This was done to set the bike for track firstly.
If you start to tinker, make small changes, and then go test em out.
It happens that the front is easier to do, but oldgixxer is right, a lot of people do the rear. I will be doing both shortly.