Hmmm, I faced the same problem.
I painted the disks with 2 pak epoxy paint until I had a fair thickenss and then lightly sanded the disks.
Then I wanted to use the same two pack to "glue the magnets down".
So I used 2"x1/4" bar steel about 2'long. Placed the magnet on the bar a few inches in from the end, and painted the magnet base with the goo.
Then (with the template in place). you can use the steel rod/bar (whatever you want to call it) pivoting from the template area as a placement tool.
You place the end on the template, and slowly lower the lever/bar down into position, using it as a 2' lever. The magnet stays attracted to it until it is on the plate, and then transfers to the plate, flat, and with the glue/epoxy paint flatly squashed out from under it.
By using thick steel for the lever, (1/4") the magnet is almost equally attracted to the lever as to the steel plate until it is firmly attracted to the plate. Then if you lift the lever up, the magnet should stay behind on the plate.
This gives total control, and allows almost flat placement.
Then I painted the magnets again with the epoxy paint, and let it pool around the base of the mags... they will never move, and should have enough epoxy between them and the steel to stop the damn rust.
............oztules