Hi,
Each eFlexPWM sub-module has PWM_SMnCTRL2, in the register, the CLK_SEL bits select the clock source. For the SM0 module, the CLK_SEL can select the IPBUS clock or EXT_CLK clock, the clock can be divided by the PRSC bits in PWM_SM0CTRL register and get the clock of the SM0.
For the other sub-module except SM0,they can select the Submodule 0’s clock (AUX_CLK) with CLK_SEL bits as 2b'10, in this way, all the other sub-module will use the SM0 clock which has been divided by the the PRSC bits in PWM_SM0CTRL register, so all the sub-module of eFlexPWM will be driven by the same clock.

Hope it can help you
BR
XiangJun Rong