One suggestion is to create a test strip with a number of pockets of varying thicknesses, then try fit to the pockets over the edge of the plywood you are using to make sure everything will fit together the way you want it to.
Say the nominal thickness of your ply is .75". In a small section of the ply, create a rectangle that is 10" wide and 5" tall. Then draw a series of rectangles that are all 6" tall (extend beyond the original rectangle on both sides), and .71", .73", .75", .77" and .79" wide (width is in .02" increments on either side of the nominal width.) A big hurrah for anyone who responds with the reason why you make the pockets taller than the test strip.
Pocket each of the rectangles to a depth of .375" WITH THE BIT THAT YOU WILL BE USING to cut out your parts. There is enough of a difference in the way that an up spiral and a down spiral machines, and machining with a climb cut vs. a conventional cut that it will affect the size of your slots/pockets.
Cut out the rectangle, then make a notation of the width of the slots before you forget what you have done. Also write down the bit you used, and the cut direction (climb/conventional.) You could get fancy and use the ShopBot to mark the width, but a Sharpie works.
When you get a new sheet of plywood, fit the test strip over the edge before you create your design files. Remember that some times, you want a tight fit (going together once, never coming apart again), sometimes a looser fit (plan on breaking down the furniture for moving to a new location, applying paint after you cut out the parts but before assembly.)
Check out the 100kSchools.org website for a picture of the test strip we made in Japan (mm instead of inches, process the same.)