Its actually perfectly easy - each pin's output can be inverted, the pins are driven in pairs (5,6), (9,10), (11,3). Invert one of the pairs,
set both to the same analogWrite value.
For the pair 5,6 you'll need this after each call to analogWrite() on the relevant pins:
TCCR0A = 0xB0 | (TCCR0A & 0xF) ;
For the pair 9,10
TCCR1A = 0xB0 | (TCCR1A & 0xF) ;
For the pair 11,3
TCCR2A = 0xB0 | (TCCR2A & 0xF) ;
Actually, thinking about this a little more perhaps you don't want inversion, you want both at the same duty cycle w.r.t ground - can't
be done in general as if the duty cycle > 50%, they must overlap. For inversion the above should work