I have done this and it works well. When you go from one board to another, you place the jig perpendicular to the edge of the board you are drilling into. You want to do the same thing when going into the 45 degree cut. The other issue is how to locate the jig between the point and the other end of the 45 degree edge. Slide the jig back and forth and observe where the hole will begin. You want to place it so that you get as much meat as you can without sacrificing meat on either of the boards. (Narrow boards could give you more problems.) I recommend you make a few tries on scrap wood before trying the final product. As a side note, I placed a screw in each board going into the 45 degree edge. I'm not sure that was necessary, but the joint was very strong. Good luck. Keep trying and don't give up.
Maybe I should ask, "can you use the jig on 45 degree cuts?"
I'm using a strip of oak 11/2" wide and 3/4" thick. I can't figure out where to place the jig, I'm using the small single hole jig. Thanks in advance for Ny help.