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I suggest if you want to manually configure the timer as per my demonstration sketch, you set the timer in one ramp mode and make the CMPASET and CMPBSET values tha same and also make the CMPACLR and CMPBCLR values the same. Then it would output the same signal on WOA and WOB or on WOC and WOD, depending on which output you activate in the TCD0_FAULTCTRL register.
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You can give it a try by trying the menu option to change the PWM pins. PC0 and PC1 is a possible choice
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see answer on question 2
