Hi,
PWM is controlled via the eMIOS module within the device. Please look at this section within the reference manual (chapter 24 Timers 24.4. The eMIOS channels will have to be enabled within OPWM (output PWM ) mode. The respective timing etc, will be programmed between this module and the clock module.
Please refer to Application Note 2865: MPC5500 and MPC5600 Simple Cookbook (go to www.freescale.com and search with AN2865) Section 19 eMIOS OPWM function. There is a code snippet which will help you understand the port directions too. (The port configuration is handled by the SIU module. The port direction and alternative functions (because the port can be used for a few different modules - table 4-3 Pg 45 in Reference manual) are shown within this example.
Regards,
Steven.