Recently I have gotten into Bookbinding and part of that is something called "Cartonage" which is an artsy-fartsy way of saying box making. In the class I was taking we made a needle case for holding the heavy needles for binding books, and by playing with the dimensions I came up with a deck box that would hold a complete deck. This avoids the double boxes that are required for carting your decks around.
Step one: Create a template
I started by using graph paper to draw out the dimensions perfectly square. Beyond using the graph pattern to insure squareness I didn't use the squares because the actual dimensions you need to make the box are slightly larger than the 2.5"X3.5" cards since the box needs to go around that dimension. The narrower dimensions you see are the thickness of the deck. Different factions can be different thicknesses depending whether or not they were from the old printers or the new printers (or how many decks you have, as some own multiple decks). Make them a sixteenth to an eighth of an inch larger than the actual dimension
You will need to cut out two of the smaller size pattern on the left and one of the larger size. You can use cardstock purchased from a stationery store, or save up some cereal boxes. What I did is place the paper over the cardstock and make pin holes at every junction. Before you cut the pieces out you will want to mark and score the interior lines. You can see in the picture below which are the fold lines. To score them without cutting them, lay a metal ruler down along the line and score it with the back of a butter knife. Then, holding the metal ruler against the scored mark, fold up the paper. take away the ruler and fold it the rest of the way and run the butter knife along the fold as if you were spreading butter. Now you have nice creases!
Step Three: Gluing
Take a cheap brush and one of those disposable covered tupperware style containers (small size is best) and add about 1/4" of glue to the container and cover when you're not using it. Start by laying out a piece of saran wrap on the table so the glue doesn't squeeze out and stick to everything, then brushing a thin layer of glue onto the center rectangle of the large piece. On top of this afix one of the smaller pieces as shown. press it down and let it dry for moment. Next repeat the step with the other piece.
Step four: weighing down for drying:
The glue will make the pieces want to curl so you will need another piece of saran wrap on top of the glued bits and then put some weights (books work well) on top of that. A good idea is to let it dry overnight and then there shouldn't be any curling.
To cut out the tongue measure down an inch along the sides and make a mark, and divide the width by three and draw two lines down 1/2 an inch. Then draw lines from the outside marks to the inside marks as shown and cut away the corners. Now place your deck inside the box and fold the sides over and then the bottom followed by the top (the piece with the tab). Note also that I cut a sort of rounded edge along the top of the groove so that it would insert easier into the groove.
In this step you lay the last piece down flat and make two marks at the base of the tab. Now take out the deck and lay the box flat with the two marks you just made showing. Cut a line between those two grooves. Now flip it back over and put the deck in the center, fold it up and insert the tab. With some practice you should get it to fit like a cardstock tuxedo.