Hi,
what do you mean by "management"? As long as you do not use special low-power modes or switching of the PLL, you just set the controller up with a special initialization sequence (which depends on type of SDRAM you use) and then use the configured memory area.
I only used Mobile-DDR SDRAM on my MCF5373L, so I am not sure if I can answer all regular or standard DDR SDRAM questions, but if you have more specific problems, I will try to help.
For switching of the PLL, I did not manage to do this myself, so I can not be of help in case there are problems in this area...
Regards,
Wolfgang