You can drill a hole thru the joist so long as it does not exceed one third of the dimension of the board. The hole also must be centered. That said you don't need to drill anything. You can lay the wires directly on top of the the joists as long as they can't be walked on. This means run the wires out by the eves, and not in the middle of the attic. You can staple the wires to the side of the joists when you need to wire out toward the middle of the attic. Also your ceiling is likely not attached directly to the joists. You can often slip the wires under the joists as well, although this can be a pain over long distances. You should also staple the wires to the joists and not just lay them up there. And as already mentioned keep the wires away from the attic access hole.
If you are determined to rewire your house yourself you should buy a good book on residential electric wiring and read it BEFORE you start. Know where you are going to put all your outlets (there are rules regarding outlet spacing), how many and how you are going to run your circuits and how to calculate box fill. There are many other things you need to understand before you start as well so read up before you pull any wire.
-rick
