In order to embed the magnet within the print, simply use your slicer to find the layer number of the layer just before the inner compartment gets sealed off on top. (I prefer to use the second-to-last layer for a comfortable buffer). You can then either add a 'Pause At Layer #' command within the slicer itself or manually pause at the appropriate time using a timer set to the layer's print time. Once printing has stopped, insert the magnet into the chamber. Be sure to double check that all magnets are securely in place and flat before resuming printing. [ If you'd rather not mess around with any mid-print pauses, use a small dab of your favorite super glue with the flush mount version instead! ]