If I run a 6 volt dc motor at 12 volts, using less than 100% PWM, will it
be ok? or will it still burn out.
If your drive circuit limits the current to the rated current of the motor,
you'll be fine, except you'll be dissipating some power in your drive by
regulating the current.
I'd have qualms about hitting a 6V motor with a 12V supply, even if you're
absolutely sure that you'll never go over 50% duty cycle - I'd worry about
the instantaneous currents.
If you know the spec - the motor is 6V at X amps, that's 6/X ohms - put
a 6/X ohm power resistor in series, and you'll be safe for sure, but
you'll waste a lot of power.
The last time I did a PWM controller, I used a current sink at a regulated
current and a supply that could be anywhere from 24-36V; I had to heatsink
the output Xsistor because it was dissipating some watts.
Good Luck!
Rich