The smaller diameter of the magnet would fit into the hole, while the larger will fit on the pad. To reflow, of course.
Could it be possible to maybe draw it, make a thru hole pad in the center of the pad, then place a cross (solder Mask) line across it so the template can be made? I don't want solder paste to go into the hole when I try and use the stencil.
Place a custom pad with the hole size you require & the annular ring around it that you require. The hole will then be drilled during board manufacture.
Diptrace will let you open up the solder paste stencil wherever you want. DipTrace will not apply solder via the paste screen into the hole itself (you can verify this by looking carefully at the paste screen
gerber - DipTrace does not show this level of detail when simply looking at the paste layer).
Alternatively, generate a non-plated through hole in DipTrace & place an annular ring around it. Open up the solder paste covering the annular ring.
Your problem lays with the infrared reflow oven. The magnet is quite large & will take quite a bit of heating to allow the solder to flow around it. The magnet material may not wick the solder well. Heating the magnet sufficiently may overheat other components on the board.
If you just want to hold the magnet in place (ie it is not actually connected electrically to your circuit), I would recommend placing a non-plate-through-hole & then using a drop of supa glue to hold the magnet in the hole.
Also be aware that heating magnets above a certain temperature will often reduce/destroy their magnetic properties.