2008 CS city water overflowing fresh water tank.

This is a first for me. I had thought that the city water and freshwater container were separate systems. When we purchased this used and hooked city water to the T@B it never filled up the fresh water container. On the times when we didn't hook up city water, we used the pump to draw water from the container. 

I see that the pump appears to be the meeting point for city water and container water. Either my pump has gone bad or something has changed. 
Now when I turn on city water, I find my freshwater container are overflowing which never happened before. If it did, that bottom would have rotted out years ago. 
Full disclosure, I used my pump to draw water from the container when I foolishly did not use the pressure regulator from the city water spigot into my T@B which blew out the poly pipes under the sink. Now that I have the pipes Hooked back up again, I'm using city water again. Except when I don't need it. 
Am I misunderstanding how this system is supposed to work? 

Pardon if this was easily searchable, but it didn't come up for me.
Sam