The manual says the max. input voltage can be up to 125 volts. your panels are 20.6 Voc (Volts Open Circuit) each. Connected in series is less than 125 volts. (84.4 volts) This would be fine if you were charging a 48 volt battery. Not a concern with charging a 12 volt battery..
The charge voltage can be selected via programming (Settings) in the controller. You can choose to charge at any of the three voltages. (12, 24, 48 volts)
In your case, you plan to charge at 12 volts, your panels should be connected in parallel. If you want to connect your panels in series to reduce the wire gauge between the controller and the panels to charge at 12 volts, you need a different type of controller. (MPPT)
What is Maximum Power Point Tracking (MPPT)