I change my filters every year. Just fill them with fuel before you put them back together.
The problem with running them in series is that unless both are running, the one stopped can block the fuel flow. Just connect them in parallel and either can supply the fuel.
Well I guess you've had better luck than me not getting air into the high-pressure side. You can draw fuel through an electric pump when it's off, as long as you get one designed to not block the flow, which the facet pump above meets the criteria for.