PWMs on TI boards are daisy chained. This daisy chaining cannot be adjusted using Embed.
Daisy chained PWMs on the F280049 board (which has eight PWMs):
PWM unit 1 is a lead unit with PWMs 2 and 3 daisy chained.
PWM unit 4 is a lead unit with PWMs 5 and 6 daisy chained.
PWM unit 7 is a lead unit with PWM 8 daisy chained.
For a lead, it should not be relative to anything (this unit can take an external input through a GPIO to trigger it).
Daisy chained units can have a phase shift relative to the previous unit (TBPHS). For example, unit 2 is phase shifted with respect to unit 1; unit 3 is phase shifted with respect to unit 2.
You want unit 1 and unit 4 to be 180 deg out of phase, but because of the way daisy chaining works, this is not possible unless unit 4 is reassigned to unit 2. Then it can be phase shifted 180 deg.