The Reds performed poorly for an hour of the match at Barnton, and found themselves 24-3 down, with only a Gareth Pritchard penalty for their efforts, before a late comeback.
That comeback saw flying winger Kyle Adams go over twice, while captain Colin Stuart and winger Mark Robertson also crossed to give the Reds a 31-24 win.
And Thomas admitted there were mixed feelings at the end of the game, having played so poorly yet still managed to record the victory.
He said: ""We are obviously pleased with the final result but feel frustrated that it took us so long to get into the game. With 65 minutes gone the game looked over for us but a great defensive effort stopped RHC from adding to their score."
"This gave the boys a lift and we upped the tempo and scored four quick tries to win the match."
Going into the match, Harry Hamilton was replaced by brother Charlie in the engine room while Alan Laidlaw's return at prop saw Colin Stuart move to hooker, with Alex Cunningham preferred to Rab Watt on the bench.
Connor Munro - Haddington's Richie Vernon having played for the 1st XV in the backs and forwards recently - made his first appearance in the three-quarters when he replaced Alex Ferguson shortly after the break.
That change saw a second-half reshuffle, with the versatile Liam Clutton moving to scrum-half as Munro took his position at inside centre.
And shortly after the change was made, the Reds ran in four quick tries, to allay any fears of defeat to the eighth-placed RHC and keep pace with the upper echelons of National Division 3.
The first of those tries came from Adams, whose brilliant solo effort gave the Reds hope, before captain Colin Stuart went over - the Reds hooker capitalising after a trademark tap-and-go penalty.
When Robertson went over, the Reds were in contention for a losing bonus point, before Adams struck and sealed the win for the county side.
And despite a below-par performance for an hour at Barnton, Thomas acknowledged the importance of another five-point win.
"There is plenty to work on but we are delighted to get five points and to remain in touching distance of the top of the league."
Thomas and his charges will now enjoy a weekend off, while the 2nd XV return to action after a week off, and they take on Dalkeith at Neilson Park on Saturday (see team news in news stories)

Haddington team: James Ferguson, Kyle Adams, Kyle Hamilton, Liam Clutton, Mark Robertson, Gareth Pritchard, Alex Ferguson; Alan Laidlaw, Colin Stuart (c), Garry Cockburn, Ben Laing, Charlie Hamilton, Jonny Riddell, Kris Paterson, Kyle McGarvie
Replacements: Alex Cunningham, Gav Stewart and Connor Munro