The phase does have a function, but unless you have the ability to measure and visualise your systems in room response, then you will have no idea what altering the phase is doing, or where to set it. Further, if your AVR has an auto setup feature like Audyssey, the processor takes care of the phase for you and you dont need to use the subs on board functions, just like with the crossover dial.
In short, the likely hood is that you don not need to do anything with the phase yourself, and dont need to worry about it.