For the advanced motor control PWM stuff, refer to chapter 36 "Flextimer Module (FTM)" starting on page 769.
There's a pretty tremendous number of features. The timer actually has 2 modes, a simple "TPM compatible mode", which is the default, and the "FTM mode" where a all the advanced features for motor control features are available (and certain registers have slightly different behavior). The mode is configured by the FTMEN bit in the FTM0_MODE register, documented in section 36.3.10 on pages 788-790. You'll probably want to turn that feature on.
Deadtime control is done with registers starting on page 801.
I have not personally used any of these special PWM features (yet), so this is pretty much all the help I can give you... pointing out the sections in the reference manual where you can find the documentation.