Control one mosfet with 2 PWM signal sources
I would suggest a scenario like this:


Cut the traces to the MOSFET's gates.
Attach those three signals from the on-board MCU to suitable (interrupt, input-capture, etc) inputs on your extra MCU
Attach PWM outputs from your extra MCU to the gates of the MOSFETs.


You can then make a decision (using what criteria is entirely up to you) as to whether you output your own PWM or the captured PWM to the MOSFETs. The latter could either be by capturing and calculating the duty cycle of the incoming PWM and replicating it with your own PWM (that would be the nicest, since you could fade smoothly between your custom setting and the default setting, for instance), or by direct mirroring of the input to the output.

Since the MOSFETs are simple open-collector sinks it would even be possible to do it without any modification of the existing board, assuming you have more suitable MOSFETs you can add to the system:







simulate this circuit &ndash; Schematic created using CircuitLab

An alternative would be to place a MUX in place of the MCU and switch between the two PWM outputs:







simulate this circuit

That method is easier to program for (no need to capture incoming PWM), but requires extra components (the MUX).