The former Norwich defender was called upon by Hughes after the Welshman got the nod at the Britannia Stadium following Tony Pulis' departure, having previously worked together at Blackburn Rovers, Manchester City and Fulham.
Stoke's first game of the forthcoming campaign comes in the shape of a trip to Anfield to face Liverpool, and Bowen was upbeat about what lies ahead.
"First and foremost you want to put your own stamp on things but at the same time, Stoke wants to be a progressive club," he told Sky Sports News.
"We want to push forward and see where we can take the club over the next few years and obviously we've got a difficult act to follow.
"Tony Pulis did a magnificent job there and we're well aware we're coming into a situation which is very stable and looks like a very welcoming place to go and ply your trade."
The duo had not worked together since Hughes departed Fulham in 2011, but Bowen says he is looking forward to getting things underway again.
"It's exciting times for myself and Mark and we're very grateful for the opportunity to get back in there and get working," he said.
"The first thing Mark will be looking to do is meet the squad and assess them very quickly.
"It's a stable squad, it's a squad of players that have been mid-table for the last three years so I don't think it needs much work done on it, it's a question of assessing the players we've got."
Winger Jermaine Pennant has signed a new one-year deal with the Potters and Bowen spoke of how pleased he was to be keeping hold of the 30-year old.
"We're obviously delighted that Jermaine Pennant has signed a contract with us, he's a player of enormous pedigree.
"Eddie Niedzwiecki our first-team coach has worked with him as a junior player at Arsenal - he's well aware of his talents as well."