I would probably treat them as two different heaters.
Create a macro to define Zone 1 as you would any heated bed.
i.e. in M950 choose your output and sensor for that section.
Then have a macro that frees the pin and sensor used for zone one and redefines the entire bed (Zone 2) using two outputs and the sensor mounted to zone two.
You could define the sensor used on zone one and have max temps etc as well for added protection.
I think that should allow PID tuning as per normal for each zone, but of course zone 1 is going to "bleed" heat into zone 2, so overall accuracy will be reduced I guess.
I'm sure it's been done many times, so someone may have more info based on actual experience.