Hi WaterModeler, I assume, by WaterCAD you mean StandAlone (SA) WaterCAD and SA doesn't understand any coordinate system or projection. What it knows is plane X and Y values. So, if two files are in different coordinate systems, in other words different X and Y then they will be drawn at different locations in the drawing. If doable, convert one of the source file's X and Y so that it will match with the other. Basically, if drawing falls at the same location without any projection in GIS software then it should also line up in SA.
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