Been across the border over a hundred times, have not had issues due to the trailer. Just be honest, have passports ready, window down, sunglasses/hat off when you pull up and don't bring guns into Canada and don't bring perishable food into US and you will be fine.
And yes RV's/TT's are in the Car lanes in all the crossings I have been to (mostly Ontario/Michigan/New York crossings). At some of the bigger crossings like Detroit/Windsor and Port Huron/Sarnia, the US side also has Truck only lanes, Car only lanes and Car/RV lanes (just watch the signs as you pick a booth).