I have a secondary transformer already which is supplying power to my 2 zone zoning board. Can I tap off of this to provide my WiFi thermostat with power or does it have to come off the furnace board?
The thermostat is going to expect to get power from Rh and C (normally), and also expect that Rh comes from the furnace power supply. So, C should come from the furnace as well. If this is for heat only, you could possibly connect the zone board transformer to Rc and C, and hook up the furnace to Rh and W and hope the thermostat gets power from Rc.
You have a few options, but you do not want to connect two transformers to Rh at the same time, and you also shouldn't connect Rh from one transformer and C from a second one.