Lightning winger Watkins was a constant nuisance to Hearts full-back Kevin McHattie and laid the second goal in the 2-0 Scottish Premiership success on a plate for McKay with a superb surge on the break.
Hughes lauded the former Hereford man's showing in the capital, hailing the display as a "man of the match performance".
McKay, meanwhile, continued the scintillating form he showed under previous manager Terry Butcher, netting two composed goals to take his tally for the season to 15 - with his 12 in the Premiership sending him four clear at the summit of the league scoring charts.
"Billy is an exceptional talent and a lovely kid to go and work with," said Hughes.
"He certainly has that quality in his locker and showed that with a great right foot and a left foot finish.
"And Marley Watkins was different class. I have a soft spot for him because he is still a young kid and has been given the opportunity to come up here by Terry [Butcher] and he really gets himself involved.
"When he plays like he did today he is a real handful, he has all the tricks - stepovers, dragbacks. If I am looking to help him along, I would just say I'd like more goals out of him."
Celebrating a first league win at Tynecastle in his managerial career, Hughes added: "It's not broke, don't fix it. Instantly, from when I first came here, I touched upon what made this club successful. And those fundamentals cannot change.
"Anything we do will be built on those fundamentals of hard work and spirit. Everything else is a bonus."