After some experimentation, I've decided it uses more energy to have the digital temp controller control my heat by turning the pump on and off. I monitor the energy use by day, and compared that method to just turning the pump to "ON" and letting the thermostat built into the heater do its job. It uses a little less electricity per hour doing it that way.
The old way I depended on the temp controller to kick the pump on, and then inadvertently the pump would kick the heater on via the flow switch. The temp controller cannot handle enough amps to control the heater directly.
I suspect this is due to the pump not turning on and off since it takes more energy to start a motor than it does while it's running stead. It's probably also easier on the pump, so I'm moving to this option. I'm just going to let the pump run and fine tune the tstat on the heater. This makes it less convenient to make changes in the desired temp but it's not difficult to crawl under and access my heater.
I also discovered it's way less economical to turn it down very much when not in use and then turn it back up before a use. After a bit of research I see that that is common knowledge in the hot tub world, but I have confirmed it

.
Soon I will be turning it down to about 85 or so I guess and just keeping a solar cover over it as summer approaches and it goes into full on kiddie pool mode.