I think it would be sufficiently less confusing if a) you didn't need a power line and b) input/output pipes were labeled somehow. So once you connect the line, you know if the end is input or output. Right now, in CR, the confusion stems mostly from having three lines, all of which have an identically-looking end (the line kit) and just the line color differs for the power line. Funny enough, the internal line objects used for pumping and power transfer have nice pictures. But they are just there for the developers :-)

Another idea would be that you just lay down the water pipes, which should be a bit larger than the CR ones, and they always transport liquid from the higher end to the lower end. A pump can be placed anywhere on the line path to set the pump direction of the attached pipe.

Even better would be if you didn't need pipes at all. You just dig tunnels and build loam bridges for water and place a pump anywhere to build up the pressure. IT would certainly make water transportation interesting and allow for complicated settlement goals. But we don't have that amount of physics in the landscape, unfortunately.