I am having trouble figuring out what relay I should be using for my solar panel set up.
I have a solar panel running to a solar charge controller. I then have the controller running into a relay. The purpose of the relay is to allow the panel to charge one of the 12V batteries while letting the load run off the other 12V battery. I then have a 12V timer switch that is connected to the relay to flip the direction of current from one battery to the other.
I have attached an illustration of my current set up that does not work. When the timer switch activates or deactivates, it does not change what battery is running the system.
I really do apologize for being a total noob, my normal work is with fish 🙂
If anyone is wondering this is for a Passive Integrated Transponder system used to monitor salmon movement. 
Best Answer
There should be no need to switch the batteries around as you describe.
It seems to be widely recommended that, in a system like this, the two batteries be connected in parallel, and to both the charging source and the load. When the solar panel is producing more current than the load needs, the excess current will charge the batteries. When the solar panel is producing less current than the load requires, the extra current will come from the batteries. The battery charge/discharge "switching" occurs automatically as the current supplied by the solar panels and the current required by the load vary.
Using the batteries this way reduces the number and depth-of-discharge of the charge/discharge cycles of the batteries and so should increase the battery life.