If this is a custom setup that does not use the standard inlet/outlet accessories you so you lose the advantage of automatic priming after setup. This is one of the main features of this filter since it makes restarting very easy after cleaning and diagnoses any air leaks on the intake side that can stop the filter canister from filling. For free help with this contact the manufacturer, Mars Fishcare. Rena Aquatic Supply offers help for custom systems. Cost is 19.95 per incident. Contact us directly with your credit card info to get started.