Part 3: Drilling holes in the body.
A good first start point, is a single body. This means that the legs will be glued on the base and that the torso (when the two halves are glued together) will be glued to the legs as well. You could magnetise these as well, but I see no point to this.
The heads can be glued on, but can also be magnetised. For the powerarmoured knights, I glued the heads on for 4 out of 5 bodies. The fifth one would get an interchangeble head (helmet option for a regular trooper, or a bare head to be a justicar).
Let that glue cure (plastic glue take a while to set, and you'll be manhandeling these models when you have at them with your pinning vice).
If you are going to magnetise your army, here's what I suggest:
BE CAREFULL WHEN YOU DRILL HOLES. THEY HAVE TO BE CENTERED!
One thing that can potientially go wrong, is to get the holes for your magnets off center. The magnets will stick to eachother, but the pose you'll end up with, is going to be all screwed up.
To increase your chances of drilling the hole right in the centre, you are going to have to work with pilot holes. These pilots holes will make sure that even the larger drills will stay centered.
Start by taking off all the moldlines and getting a nice flat surface for your shoulder sockets. Then, with your sharp craft knife, try and find the centre spot of the sockets, and make a tiny indentation in the centre.
Even when using the smallest drillbit you have, you will have a hard time staying on centre, and you can be A LOT more accurate for this with your craft knife. After this indentation has been made, get the smallest drill out that you have, and drill into the body. Use this indentation as a guilde for the drill. The body will need 3 (of 4, depending on wether or not you want interchangable heads) holes drilled into it. One in each shoulder, and one right above the “bulge” where the backpack is going to end up.
After you made these pilot holes, it's safe to have at them with the 2 mm drill. If you notice these aren't exactly on center, you can still do SOME correcting with your craft knife by making the whole slightly bigger towards the center.
Then drill the hole with the 2 mm drill. Don't make this hole to shallow, or your magnets will sit “over” the surface and the pose will just end up looking weird. Don't drill to deep though, you'll run the risk of drill straight through the miniature, because these drill will go through plastic like a hot knife through butter! This is what it should start looking like.
Now on to the next step: Adding the magnets.