There are two steps to setting up a lock miter bit.
The secret, (at least for me), is to figure out where the center of the bit is. I use a digital height gauge and measure the distance between the two horizontal 'flats' of the bit. So on my Bosch bit, the distance is 0.354 so the center of the bit (that actually does the cutting is .177" down from the top flat.
You want to align the center of the bit with the center of the thickness of the board. If the Board is .75" thick, center would be .375" either up from the table. I have already worked this out with my router bits and shaper cutter, and I know if I am working with a true, 3/4" board, the top flat of the router bit should be at .552 above the table
Next you set the fence. Put one of the boards on edge, up against the fence along with a straight edge. Position the fence so there is just a tiny gap in between the cutting edge of the bit (90 degrees straight out) and the straight edge.
To check to see if you have the proper bit height, take two test pieces, lay them flat on the table and write UP on one of them. Run both pieces through (flat on the table, not on edge) and then mate them together, with the UP piece UP. If the UP piece is higher than the other piece, the bit needs to be lowered, about half the distance of the step up.
It seems like a pain, but you only have to measure your bit once and then make adjustments for the actual thickness of the lumber you are using