Measure the width of the two beams. Mark the width of the first, overlapping, beam on the second beam with a square, drawing both lines across the width. Turn the second beam on edge and transfer the width lines to the edge. Do this for both sides. Repeat this process on the other beam if it will be notched.
Calculate the depth of the cut -- cut away no more than half of a beam's thickness. If two beams are of equal thickness, notch halfway through both beams to make the beams flush with each other at the joint. Mark the cut depth between the marks on the sides. Cut away less material to preserve more of the beam's strength, which is important if the joint will not have other support.
Set the cut depth on the circular saw to the cut depth marked on the side of the beam. Cut across the beam just inside both marks and preserve the lines -- you can always widen the notch if necessary but you can't make a notch narrower. Make multiple cuts approximately 1/4 inch apart for the entire width of the notch. Complete this process for both beams if they will both be notched.
Chisel away remaining material and make the inside faces of the notches smooth. Do this for both beams if you are notching both. Test fit the joint and make adjustments using the circular saw to widen a notch and the chisel to make adjustments to the inside of the notch face.