You can run the drain on both systems up and then over. There is however a limit to the rise. I have always know do not run a drain line up more than 8' above the valve. If you have a long run, make the run in a bigger tube or pipe. The connection on a Fleck 5600 is 1/2", so if the run is long, convert to 3/4". PVC will work fine for this. Does the area you plan to install in freeze? If so, you need to prevent the media tank and drain line from freezing. I would stay away from the GE unit.