Is this what the tunnel tokens are for?
I place the tunnel tokens on the tunnel once I put the tunnel on the board. As soon as any company runs though the tunnel, I remove the token from the board and place it on the tunnel company card. This allows you to track which tunnels have been used so you know if the tunnel card pays the owner each round.
I do the same thing with the mountain companies.
I've no idea if that is what the intended purpose of the tokens are as I didn't see that addressed anywhere in the rules, but it seemed like a good use of them to me.