Dowels can be used in different ways to reinforce many different kinds of joints.
Through dowels are drilled from the outside of the assembled joint, leaving the dowel visible. Blind dowels are drilled from each inside face, so that they are invisible when the joint is assembled.
Depending on where the joint is located and how its oriented, you can employ different techniques to accurately drill the dowel holes. One commonly used option is the self-centering doweling jig, which helps position the hole in the center of the workpiece's thickness. Other times, it's best to make a custom drill guide for a specific situation.
This is an example of a blind face-frame doweled joint. That means the dowels are not visible from the outside, and the two boards meet end-to-edge.
When using dowels to reinforce a butt joint (that is, a joint where the two pieces simply *abut* each other without any interlocking joinery), make sure the pieces fit together well as a starting point. Make a marriage mark or otherwise label to keep track of how the parts go together. Decide where the dowlels will go and make a tickmark across both parts. Also decide and mark how deep the dowel will go in each part (this may be asymmetrical, depending on the joint). Use a combination square and a sharp pencil to carry these lines around the edges/ends/faces of both parts.
Choose the dowel's diameter. The general rule is to use dowels that are about one third of the thickness of the wood pieces. So for 3/4" thick material, use 1/4" diameter dowel.
Gather the tools you will need: dowel, drill bit, and drilling jig in matching diameters, as well as a hand-held drill.
Secure your workpiece in a bench vise. Use the self-centering doweling jig, which ensures that the holes are positioned in the center of the thickness of the workpiece. Use your layout lines to position the jig laterally.
To place the doweling jig accurately, sight through the window at the white lines scribed on the inner block. Also make sure the jig is sitting flat on your workpiece--if it is crooked, your holes will be too.
It is important to drill to the correct depth. Based on your layout lines and the height of the jig, put a tape flag on the drill bit. The conical tip of the bit should extend past the depth mark.
Install the drill bit in the hand-held drill. Make sure the settings are correct: top toggle switch on 2 (fast mode), torque ring twisted to drill mode (picture of a drill bit), and drill in forward (arrow pointing towards front of drill). Note: always run the drill forward, even when backing out of the hole. No need to put it in reverse.
Seat the drill in the jig, pick it up slightly, run to full speed, then plunge down to the flag. If it slows down or stops cutting, pull the bit out and clear the sawdust.
Mark and cut the dowels to size. Use a handsaw, bandsaw, or the mini chopsaw. Chamfer the ends of the dowels with a sanding block.
Test the joint before adding glue. Make sure it can close all the way with no gaps. If there are gaps, figure out the causes and address them. Common issues include dowels cut too long, sawdust in the holes, poor inital fit between parts, etc.
In this example, the end of one piece meets the face of another. This arrangement of parts requires a different technique. The end-grain can be marked and drilled as above (using the doweling jig), but the face grain cannot.
One option is to simply rely on good, accurate layout on both parts. Use an awl to dimple the center of each hole, which helps the drill bit start accurately without skating around.
Another option is to drill the end-grain, then use hardware called "dowel centers" to punch transfer marks to the mating piece.
Because the centers hold the two pieces apart, it is difficult to make sure they are aligned accurately. Clamp battens or guides as needed to help place the pieces properly before striking to transfer.
To drill the face, use the drill press with the depth stop, or a hand-drill with a tape flag.