A number of bosses – including Steve Lomas of St Johnstone and Kille gaffer Kenny Shiels – have lashed out at whistlers this term as the relationship between those in the dugout and the men in the middle seemingly deteriorates.
Thomson said: "It's important that they show restraint, because it doesn't do their team any favours, nor does it do themselves. It's important that we do build that relationship.
"I think we're coming together a lot closer. We ran a campaign through the Scottish FA to go into every club and speak to every player and every coach last season.
"And, when coaches or managers want us to go in, we'll go and speak to the players.
"That's an important part of the game, because we give them, hopefully, an understanding and an interpretation of the laws of the game.
"What you will find with the top referees in Scotland is that they will give the opportunities to the coaches, to the managers, to come and speak to them.
"We're happy for the coaches to come in after the matches. Provided that they come in in a reasonable manner and they show the respect, then we're happy to explain that decision.
"I'm not going to say they always agree with our decisions, but I think it's important we're there to explain the decisions to them.
"I think certain managers this season will look back on some of their actions and some of their comments with regret, whether it's the end of this season, whether it's in a few years' time."