Hi,
Regarding the required PWM waveform of totem PFC, as the following figure I copied from AN12618.pdf.

You have to use the PWM_SM0_A and PWM_SM0_B signals to control the Q1 and Q2, the PWM_SM0_A and PWM_SM0_B signals are required to be complementary, this is so-called 180 phase-shift PWM signals. In other words, the Q1 and Q2 must be connected to the A and B of the same eFlexPWM sub-module PWM_SMx.
Regarding the SD1 and SD2 power device, you can connect them to another A and B of eFlexPWM sub-module, for example PWM_SM1_A and PWM_SM1_B signals, I think connecting GPIO pins to SD1 and SD2 is okay. As you know that eFlexPWM module supports software control mode, in other words, you can set/clear the PWM_SM1_A and PWM_SM1_B signals with software. In a main power half cycle, for example above a and b figures, you can clear the PWM_SMx_A signal to low to turn off SD1, but set the PWM_SMx_B signal to high to turn on SD2 in half main power cycle.
Hope it can help you
BR
XiangJun Rong