Put all your pedals out on the floor how you would place them on the board in two rows (one for the top row, one for the bottom), leave an inch or two between each one for a patch cable. You may want to leave a little extra room for one or two additional pedals you may pickup in the future; measure the dimensions.
Use a protractor to measure a slight angle for the small blocks of wood that will support the second level. Make the blocks about an inch shorter than the width of the top level. Go to a local hardware store and have two pieces of 1/2 inch to 1 inch thick plywood cut. Then have three little blocks cut out at the angle you measured earlier. Buy sand paper, sand the boards, nail or drill them together, then spray paint it black. Buy some velcro and you're set.
Total cost: about $25
Total time: about 2 hours including the time at the hardware store.