I’m going from memory, and using a spindle moulder lock mitre block rather than a router bit, however the principle is the same I believe. They should be simple to set up taking no longer than any other cutter.
First set the height of the cutter to get the interlock roughly central in the joint. Preferably so that the eye can’t see it not being central. Adjust the infeed fence so that with the board when laying flat on the table the cutter takes off only enough to cut exactly from the top to bottom. The key is that the Edge to be mitred is square and true. The cutter must not cut away any of the top edge after the cut is made. I.e. the board will run through the cutter with an outfeed fence set parallel with the infeed without the cut getting deeper.
Run your first part for the joint through, face down on the table. Now run your second board through face against the fence. They should be a perfect joint.
If you don’t have a perfect square and true Edge before it’s to be machined it will become a tedious exercise of futility.