Wow that turned into quite the discussion. After additional research, I agree with the one pump being discontinued theory. I can only find one pump and the line has been teed off. I also found that at the top of the tanks where the water comes into the wells, in a place you can only feel but not see, there is a quarter turn lever that shuts the flow of water to each particular tank. That way even with one pump you can direct which tank, or both, you fill.
Thanks for all of the input and ideas about the plumbing, how to best keep your catch fresh and ways to prepare them for eating. You guys are great.