Lee Highfield and Pat Walsh had given Upton a 2-0 interval lead before Luke Jackson extended their advantage to 3-0 after the break.
Ali Hallal and Warren Roberts reduced Waggon's arrears, before Mike Bowell clinched victory for Upton near the end
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Crossway edged their way through to the second round of the Chester FA Senior Cup after a 3-2 win at City Bar.
Pete Syddall and two-goal Phil Goss accounted for the Crossway goals, while Paul Head and Lewis Carter replied for City Bar.
Chester Nomads produced a convincing 7-1 home win against Robin Hood, with Mark Crossan, Gary Riley, Lee Owen, Andy Mitchell, an own goal, and two-goal Mike Jeffs on target.
Warren Fowles and Ian Hughes combined in Hoole Rangers' 2-0 home win against Saughall Thursday.
Tarporley Vics had Ed Patterson grab a hat-trick alongside Henry Buckley in their 4-0 victory against Barrow Athletic.
Frodsham United edged a 5-4 win after extra time at home to Uberlube, with John Potter, Mike Dober, Graham Dickson, Anthony Gobin, and Jimmy Leck accounting for Frodsham's tally.
Adam Langton and two-goal Chris Larson scored for Highfield Athletic in their 3-2 win at Tarvin 2000 Athletic who had Adam Crimes and Stuart Groves hit replies in the Premier Division clash.
Nathan Mapletoft, Gaz Holmes, Mike Edwards and Adi Callighan scored for Newton Bears in their 6-4 home defeat against Kelsall.
Duddon United scored a 4-3 win at Chester Nomads thirds in Division One, with Lee Gilordo, Craig Matherson, Shaun Roberts, and Danny Cookson all on the mark for Duddon, and Jon Roberts, Martin Moore, and Jack Delgardo scoring Nomads' replies.
Richard Deponeo and two-goal Adi Gough scored for Cestrian Alex in their 3-3 home draw against Ashton Lions who had Richard Preston, Ian Mahugh, and Lee Williams on target.
Terry Ellams, Matty Cotterall, and two-goal Matty Sharlock scored for Chester Nomads IV in their 4-0 win at Vicars Cross Doves in Division Two.
And Paul Joiner grabbed a hat-trick for MBCS in their 5-1 home win against Boughton Athletic, with Adi Martin and Paul Bennion adding the other goals.
Adam Critchlet bagged a hat-trick for West Meters alongside Dan Cullen in their 4-2 win in Division Three against Saughall Thursday reserves who hit back through Phil Lloyd and Gary Owen.
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