The single VR sensor input is for something like a 36-1 trigger wheel. It has 36 teeth, with one missing. The ecu sees a pulse every 10° and when it sees the 20° gap it knows it is at TDC, so it starts a new cycle.
Let's ignore our stock distributor, there's literally no reason to keep it, let's assume you use the Miata CAS (cam angle sensor) It bolts right in place of the stock distributor.
It has a 4/2 trigger wheel. A two tooth wheel gives a signal at TDC, starting the cycle (I believe one pulse is longer than the other). The 4 tooth wheel gives pulses every 90° aligning with each cylinder's firing.
It's much lower resolution but for running batch fire it's fine, you may be able to do sequential injection/ignition with it.
These signals are called CMP and CMK and require two separate input lines into the MS unit instead of one. It has to be configured for the two inputs at the circuit level.
You can tell your ECU builder that you will use the 4G63/miata CAS as the trigger.
This stuff is the heart of the ECU, I would recommend a pile of reading on how the Megasquirt works and relies on the sensors. There is a plethora of documentation, specifically for the 1.6L Miata that will be helpful. Here's a start:https://www.diyautotune.com/support/tech/install/mazda/megasquirt-your-miata/
You can use the stock Miata coils but the COPs would be a little better, read the warnings on the page about the stock miata coils.
The settings/configurations on that page are necessary, you will probably have to configure it yourself when you get it