> How is a beat presented to the processor? Digital input goes HIGH?
Using an analog input "above threshold" from a hardware peak detector with some software debounce.
The processor has an analog comparator capable of generating an interrupt that may help. It would be especially easy to use if debouncing was done with hardware.
As for the PWM outputs, they use interrupts, ...
Nope. The pin state is changed entirely by hardware.
...and if I designate an interrupt for my own use I have to give up one of the PWM pin pairs, correct?
If, for some reason, you need to use a timer then you may have to give up a PWM pair. At this point, there is nothing in your description to indicate the need.
> They (looping functions) are all at least one order of magnitude faster then you will need."
If I start nesting loops and performing operations in the loops, I am concerned I'll start missing beat triggers, ...
In which case, using an interrupt is a good choice.
...but the operations (counting, comparing, etc) are likely much slower than the loop functions so I shouldn't be concerned about looping time. Beats typically are at least 400msec apart so should be plenty of time between them.
(400/1000)/(1/16000000) = 6,400,000 clock cycles; 3.2 million to 6.4 million machine instructions.