Yup run them both.
An aircraft has a mag switch for applying the ground to each mag when you want to run the engine. The aircraft switch is normally labled (L) or (R), left or right, and the purpose of even having that is to allow a quick mag-health check. Once the engine is warmed some at just before takeoff ya "kill" one mag at a time and look for a slight RPM drop compared to running both. anything in the neighborhood of 1k RPM is grounds to terminate the takeoff and return for maintenance. Seems I remember the Skylane O-470 dropping around 3-400 RPM at mag check, been a long time though. The same can be done in you airboat. There is no reason to not start and run the engine on "BOTH" mags.
Scotty