Solar power question

[Mikeg]

I apologize in advance as I'm sure this has been asked so many times, people are likely sick of it. I have 2 x 12 volt batteries wired in parallel. I bought a 40 watt crystalline solar panel with a charge controller. So, I ran the positive and negative wires from the controller to one battery. I never got a charge in the batteries according to the built in push button battery indicator(which I know is not likely highly accurate) of more than 2 thirds full? I do get a reading of full charge after plugging them for a night. Do I actually wire it as above or do I hook the positive to one battery and the negative to the other? And does the charge indicator in the trailer not pick up a full charge from the two batteries or just one? Thanks so much.