are the Arduino "interrupts" just logical numbers that map to a different real interrupt?
Bingo.
Also digital 0 and 1 (Rx0 and Tx0) are shown as PWM on the schematic, presumably this just means that you can do a digitalWrite() as there's no hardware PWM support on these pins.
I think this is a schematic labelling error. Those pins (PE0 and PE1) are not connected to timers thus do not support PWM.
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The Rugged Motor Driver: two H-bridges, more power than an L298, fully protected