In case you didn't get my response.
Hi Doug, Yes you can splice in the MPPT controller between the SAE port (with solar panel) and the battery. When you say Master Power Switch I assume you mean the battery switch. Typically solar charge controllers are connected between the battery switch and the battery, so charging can happen even with the battery switch off. The rooftop solar is connected this way. It's not a big deal to have the controller on the downstream side of the battery switch. That is, with the battery switch off, the secondary solar panel won't charge the battery. You can confirm this is the configuration by checking the voltage at the SAE port with the battery switch ON and OFF. Connect the wires from the SAE port/solar panel to the PV terminals and the wires going to the battery switch or battery to the BATT terminals. I would double check the polarity of the wires from the solar panel and SAE port as the polarity can get reversed depending on how it's installed. If the wires going to the battery are anything smaller than 10 AWG, you should consider upsizing them sometime to get better/faster charging efficiency.