You can't rub a doweled joint, but that's somewhat the point. The dowels add both alignment and moderate strength. First, however, the holes for the dowels have to be aligned in the two sides of the joint. Here are two methods to try. First is the brad-with-the-head-snipped-off method. Wherever you want the dowels to go in one piece, tack in a brad. Don't drive it in much more than 1/4 inch. A brad is just a headless wire nail less than an inch long, so you can easily cut it with a pair of nippers. Nip off the brads so that only about 1/16 of an inch remains above the surface. Align the two boards and push them together so the brads in one will leave impressions on the other. Separate the boards, pull out the brads by gripping them gently with the nipper, and you have the marks to start your brace and bit.
The snipped brad method is wasteful but handy. The standard method uses a try square and gauge. Clamp the two boards upright in the vise, face side to face side, the edges to receive dowels upward. Mark across both pieces with the try square at each dowel location, but only with a small mark across the crack between the boards. Separate the boards and, with the stock of the try square pressed against the face side, extend these lines across the edges. Now set the gauge for half the thickness of a board and, gauging from the face side as always, mark this line across the previous ones.
With your dowel centers so carefully marked, take care that you bore the holes straight and deep enough to give a slight clearance at the bottom. The holes, and the dowels, of course, should be about a third of the thickness of the wood. Any wood upthrust by the auger will keep the joint from closing, so cut away a little extra countersink around the top of each hole with a knife. Each dowel needs a saw cut down the side to let trapped air escape, so hold a saw held upside down and drag the dowel along it—just like a cooper's jointer. Check the dry fit of the pieces before gluing and clamping.
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