Magnetising is actually a pretty simple process, and at it's most basic you only really need a few items. The magnets, and an appropriately sized drill bit. I've used 3mm magnets for regular 40k things (such as a Vendetta conversion) but given the size & bulk of Krull I bought some 6mm ones. (Also, they brought a Flames of War order up to free postage level and helped me get the third edition rulebook for free!) When they arrived it turned out they were closer to 5mm, so I pulled out the necessary bit from my DiY cupboard.
Magnetising flat surfaces is probably the easiest. Simply drill the hole. Don't go deeper than the depth of your magnet. Remember that the drill bit comes to a point, so the hole will look deeper than it is. Then, fill the hole with glue and slide the magnet into place.
The principle is exactly the same for the second magnet on the adjoining part. The difficult part, is making sure that the two magnets will line up as perfectly as possible. You magnetise because you want to play with the kit and transport it easily... but it will look awful if the visible sections of the model are mis-aligned... and you won't be able to hide any joins with modelling putty! However, you can still use that putty to help you create a guide so that your magnets WILL line up.
Place a small amount of putty onto the side that needs drilling. Wet the side with the magnet (to stop it sticking) and then marry the two up. Because the putty is soft you can move the parts to ensure that they line up externally. Separate the parts and you will then be able to use the marking as a guide. Later, you can remove the putty, or, depending on the pieces, you may keep it in place to help provide a flusher fit between parts.
I done exactly the same with the wings;
Simple! ... Well... yes, and no. It turned out that the larger magnets, whilst great for holding the weight of the beefy arms, were not quite strong enough to fight against gravity when it came to those massive, highly detailed wings!! Come back next time to see what I've done to try and improve the situation... and one way you can overcome another issue that comes with magnetising...