These are the magnets I am using and I managed to grab a drill bit that is the perfect size for the magnets. It is easy to drill into the resin with this drill bit, but very difficult to drill into the metal of the turrets (if you are using non CoA ships). I did purchase some even smaller magnets previously, but the company I bought them from now want some ridiculous amount to transport them to Australia, so I've had to move on to these magnets.

I had already magnetised the turrets as these also get knocked off anyone wants to take a look at your ship, but the turrets are easy as there is only a single point to magnetise and it is easy to line up the magnets. However the two sections of the battleship are both fairly large and so my first attempt at aligning the two pieces ended up with my mangling the middle part which you can see in the image at the top (and the one to come below). A single magnet was also not quite strong enough to hold the top part on.

Then I stopped being stupid and realised that I could put some paint on each of the magnets on the top part and use that as a guide as to where to drill in the bottom part. I still had a bit of trouble with one of the locations, but I just enlarged the hole and made sure to put the magnet in the right spot.

A toothpick was quite handy in moving the magnet around and ensuring it was flush with the surface.
If you do stuff it up, don't worry as there is plenty of space available to try again.