The water pump does have a check valve so water will not be able to flow through the pump and into your fresh water tank. Also, the water line running from the pump to the city water valve should also be correct. Turned one way it would allow city water into the coach (not the tank) so you don't need to use your holding tanks or pump. Turned the other way you would be using your holding tank water and water pump as your pressurized water source. There should either be a third option on the valve (fill) or a separate connection somewhere that gives a fill option. Is there no "gravity fill"? I am assuming not since you say there are only 2 lines connected to the tank.
If you can fully see all 4 sides of the tank and the only 2 connections to the tank are the 2 lines that run directly from the tank and out the floor as drains then someone has really screwed something up.
