The cell should definitely be after the filter. The Autopilot manifold does contain a screen to stop any large debris from making it to the cell itself, but I haven't seen that feature in any other SWG. My temporary plumbing for my solar is coming off between the pump and the filter and the amount of junk the screen in that line catches is surprising, I can't imagine any other solar cell surviving for very long in-between the pump and the filter.