To make the grooves necessary to flush the braces, we need to mark out our cuts. So center your braces, and mark on each side where the boards meet. (See above).
In the above photo, you can see the line we just marked on this bottom board. Notice the top board - there are two more lines and an X. The X tells us where to cut, and the lines show us how wide and deep to cut. We are going to make a groove (dado) that is 1/2 as thick as the board.
Before taking boards over to the saw, mark the boards so you remind yourself how to put things back together. Notice below, I put an "L" on the board for a reminder (see below).
