First you'll want to remove the screw from the Hobby Creek Arm. Use the T-15 bit, and set the screw aside. You'll use it later. (NOTE: This may not be a T-15 screw, but a T-15 bit works.)
When orienting rare earth magnets, it doesn't particularly matter what orientation the magnets are (North or South) academically, what matters is that the sides match up per piece. Both magnets on each piece should be the same orientation, and the pieces themselves are opposites of one another? Confused? Excellent.
To start, use a sharpie to mark the top of two magnets that are the same orientation.
There are tiny detents in the plates, to allow there to be a layer of glue underneath the magnets, while still keeping them flush with the top.
When applying the glue, use the brush to layer in a thin coat. The magnet is a tight fit, but won't require deformation of the plastic to stay in. It isn't a full press fit, because you do need the glue in order to keep the strong magnet from wiggling out.
Press the sharpie side into the space, so that the clean side is facing out. Go around the outside edge with the fine precision CA glue, and leave a thin bead.
Use a cloth (paper is fine) to remove the excess CA glue from the top of the magnet, or it will frost when dry. Example below.
Once one plate is complete, orient the next plate so that the spaces are aligned, and then place a magnet onto each of the glued in magnets. Use a sharpie to mark the exposed side. Now glue the marked side down into the space on the other plate, as before.
Screw in the threaded side of the Hobby Creek Arm into the center of the mounting plate.
Place three dabs of glue onto the sides of the printed knob, and put the bolt into the setting. Then remove the now-glued bolt, rotate it 60 degrees, and put it back into the knob. Now all 6 sides have an adequate amount of glue around the bolt top.
Attach the bottom plate to the Hobby Creek Arm, using the original screw. OPTIONAL: Use an O-Ring inbetween the arm and the plate.
Attach your camera to the top plate. In my case, I use a Canon Powershot S110, and the plate is designed to allow access to the bottom door for battery and SD card.
Clamp the mounting plate to the edge of your workbench, table, or whatever surface you like.
Snap together the two plates with the magnets, and you're ready to go!
The largest object is a stand, for supporting the Loc-Line arm if you need to extend it out horizontally. Loc-Line is fairly stiff, but if you push the mass over too many links, it'll bend. The little support made it so I can get very tight shots.