Find a drill bit that matches the size of the magnet. I found this one in a set of assorted drill bits from very small to this size as one of the largest.
See how the width of the drill and magnet are the same.
Using a hand drill a hole into the arm and the body. When drilling into the arm take care to drill just enough for the magnet to slot in, any further and you could drill out the other side. If this happens, just make sure you don’t have the pads on, you can green stuff it and cover it up if needed.
Do not use a dremel or any other type of electric drill as this would melt the plastic and could rip right through the model.
Take a toothbrush or some other soft item that will allow you to push the magnets in and it won’t stick to. A little firm force is all you need to press the magnets in.
For the first model, press a magnet in using the toothbrush, once this is done, just attach a magnet to the torso now. You may need to take a screwdriver, butter knife or something else to stick the first magnet to slot it into the body. Once it is in partially, you can disengage the metal object from the magnet and use the toothbrush to finish.
Slide the arm away after you press in, leaving the magnet behind.
Press the magnet in with a gentle and firm pressure.
Then take the torso and attach a magnet to the one you just finished with. This is to ensure the poles match up and make the arms able to change out. Take an arm and press the shoulder where the hole is drilled into the other magnet using a gentle but firm force. Then use the toothbrush or whatever you are using to finish pressing the magnet in to a flush position.
Line up the poles of the magnets.
At this point you now have a finished set of arms and a torso. Using the torso you can finish making the rest of your arms and the arms can be used to press the magnets into the remaining bodies of your terminators.
Pressing the magnet into the arm.
Line up and continue to press the magnet into the hole.
Remember also to use a solid body and arms (like power fists and combi bolters), this helps to avoid bending or snapping a power weapon/thunder hammer. Also swap out torso and arms to avoid putting constant pressure on a single model. They are plastic and can only take so much force. Too much over a period of time is a bad thing and could damage a model.
In the event a drill point was not perfect, you could use a dab of glue or a small ball of green stuff to help hold the magnet in place.