To cut a lock miter joint on the Router Boss you need the optional digital depth gauge kit ($32) plus the included stop and aluminum router plate guides. There are 2 settings: depth of cut and thickness of the boards.
With one of the boards clamped flush to the bottom of the base plate, zero the cutter on top of the wood. Divide the thickness of the wood + cutting length of the cutter by 2 to get the plunge depth. This will put the center of the cutter at the center of the board. Move the cutter away from the wood then take this plunge using the digital depth gauge. Lock your plunge router at this depth.
With the board still clamped flush to the bottom of the base plate, zero the cutter against the edge of the wood and lock the router plate at this position. Use the mating board to set a stop in the guide rails that will allow the router plate to be moved forward the exact thickness of the board. Remove the board, bring the router forward to the stop and again lock the router plate. Your setup is complete.
Cut one board edge by feeding the wood horizontal through the cutter then cut the mating board edge by feeding vertical through the cutter.
You should make a trial cut in scrap, but the setup will be close to perfect. This setup is much more precise than the typical setup on a router table.