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 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."
As well as suffering another defeat which leaves Hearts marooned at the foot of the table, still 14 points behind Ross County, the home side also suffered another injury scare.
Jamie Walker was withdrawn at half-time with an Achilles complaint and Locke admits the winger may be the latest name added to a growing injury-list, with Ryan Stevenson, Jason Holt and Mark Ridgers already on the treatment table.
"It never rains, but it pours," said the beleaguered Tynecastle boss. "If there's one player at the moment who looks a right good goal threat for us, then it's Jamie Walker - and we lose him.
"With Ryan [Stevenson] out, that's two players in a small squad who are capable of getting us goals. To have the two of them missing was a blow for the second half.
"I certainly hope not, but it's an Achilles injury and we might have to wait another 24 hours to see what happens."
However, Locke believes his patchwork Jambos were well in the contest - but for the quality of McKay.
He explained: "I thought we contributed to the game but the difference at this level is in the final third and they have a player who can score goals, Billy McKay."