As Simonmd said, at the moment there aren’t waypoints to use with buses and trams (as the signals waypoints for trains), so the only way to avoid two or more routes colliding and causing jams is to plan accurately every route and the junctions between the routes.
My method is to place two pair of stops for every road before the crossing where two routes merge, and then group them in a single stop. The two lines would then automatically choose the nearer stops (which are the ones on the road from where the route comes), and don’t jam the crossing. I use the some technique for route terminus, i place two separate stops on different but adjacent roads.