How do you generate the PWM output (which hardware subsystems do you use)? 
And how do you controll them (by which software)?

When you use the PWMSS subsystems (either eCAP or PWM modules), you can 
synchronize two subsystems by setting some bits in the control registers. 
See SRM <http://www.ti.com/lit/pdf/spruh73> chapter 15 for details. Ie. you 
can use libpruio <http://beagleboard.org/project/libpruio/> for easy access 
to those registers.

BR

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