There are two major sizes that you'll want to use for magnetizing a Knight model, Especially if you want to model on additional weapon mountings, should you be attracted to the Forgeworld Knights.
The first and primary size of magnet you're using for something that size will be 5x2mm magnets. You can use these to magnetize the arms to allow swapping. My technique is to slice the arm on the vertical section, where the shoulder piece meets the rotator joint for the arm that allows it to swing outward. Cut off the plug on the weapon side, and use it as a cap, to give you a better position to fix the 5mm magnet in place.
The 5mm magnet is also small enough it fits into the socket on the top of the carapace so you can get a good hold between the carapace and its weapon options.
The other size of magnet you will want is the 3x2mm, which is useful in any number of fitting solutions you have. You can use this for magnetizing the swap of the Meltagun and the Stubber from the inward mounting.
If you drill very carefully, you can get the magnet into the larger diameter piece of the weapon mounting so there is some of the plastic still there to hold the magnet. You can then just fix the other 3mm magnet into the mounting ring for the weapon with a minimum of work.
The ultimate complexity comes with magnetizing the weapon arms if you want to swap in the Forgeworld weapons. I have the Styrix, and have done this.
The melee arm is actually very easy to work with, as you can slip a couple of 3mm magnets into the weapon elevation joint and add a couple of 5mm magnets into the arm ends so it holds smoothly. I pinned the rear piston into place so it actually stops the arm from sagging down in place - no magnets, just the resistance between the chainsaw arm and the piston - the resin arm makes a nice cup once you trim it down inside.
The main weapon is a bit trickier, but similar. Before you close up the weapon mounting, make sure to carefully drill the magnets into the weapon arm, I used 5mm on the arm, 3mm on the gun, because there isn't a lot of material either side of the weapon on the big volkite gun. They'll hold secure, and of you pin the two pistons that would take the role of "elevation piston" on either side of the lower arm, it'll help reinforce things.
I loose-pinned so I can just slip the pistons off and switch gun mountings in short order.
If you absolutely need, I can snap a few pictures for some clarification.
A lot of my initial reading was from this article, which is rather good for information.
http://fromthefang.blogspot.ca/2015/06/magnetising-imperial-knight-warden-kit_20.html