The pair have replaced Glenn Eldridge, who stepped down earlier this month.
It is the dawn of a new era for the Shrimpers, who will be playing back at Step 6 level next season in the new division having previously been in the Essex & Suffolk Border League.
Manager Shelley and assistant Wallace made no secret of their desire to get back in the game, having left Clacton in February.
They spent the end of last season helping out at Cornard United.
"I'm really pleased," said a delighted Shelley.
"For me, Harwich is still one of the biggest clubs around in terms of our local football scene.
"They want to progress but it's also a club with a real history.
"Mike and I can't wait to get started."
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