I am using the Nyko PS3 dongle and what I have found is that if I turn on the PS3 with the PS3 controller then the controller will always take controller assignment #2. However, if you turn the PS3 on via the power button on the counsel or by inserting a disk and then wait for the PS3 to boot up (past the audio chimes), then press the PS button on the controller, the controller will take controller assignment #1. If you turn on the controller before the chimes, it will take controller assignment #2.

Bottom line solution.
1) Manual press the power button on the counsel
2) Wait for the chimes (boot up to be complete)
3) Press the PS button on the controller