Recommend slicing as desired, then modifying the gcode to execute “M0” before the layer starts covering the hole. If your firmware supports it, it should auto-pause, allowing you to insert the magnets, and then resume the print.
The magnets used are rounded and 25x3mm.
The author remixed this model.
Remixed the XL version of this STL to hold the magnets internally.
The holes are 26 mm in diameter, giving plenty of wiggle room for the magnets to fit.