Glad to hear you have made some models. The magnets can be held in place by either pushing them directly in the holes, or using a bit of glue if the holes are a bit loose. Results depend on the quality of your printer and the tolerences in the print and magnets. Some of the magnets i used were much weaker, so I didn't have so much of a problem. If yours are too strong, perhaps try only putting every second or third magnet in.
Good luck with that!