Played in a heavy downpour, Michael Beale took the opportunity to give some of his squad vital minutes as the likes of Andy Firth, Kane Lewis, Nathan Phillips and Jake Brimmer all returned.
Toni Gomes netted the first goal courtesy of a Madger Gomes assist and Madger then scored the second himself.
Glen McAuley, who has made a habit of finding the net at an impressive rate for the U18s so far, came on as a second-half substitute and had a goal disallowed.
Reflecting on the game, Beale told Liverpoolfc.com: "First of all I would like to thank Runcorn FC for agreeing at late notice to playing this fixture after our original opponents TNS had to pull out.