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Generally, P4 coolers can be mounted when the mobo is already in the case, whereas AMD coolers must sometimes be mounted outside. The reason: a lot of socket-7 coolers need to be wedged on with a screwdriver, and the case tends to get in the way.
Generally speaking, you'd want to use as many as 8 to 10 spacers between the motherboard and the backplate - there shouldn't be any possibility of moving the board "up and down" when it's in. If you can't use screws in certain locations, rubber sticky cones are usually supplied to solve that.
The best advice I can give you, is to READ THE MANUAL. It's the one thing that you can do to prevent damage... The most difficult bit these days is probably the connectors for the case (power button, lights, etc) - they're kinda difficult to place right if you've never done that; but if you do it wrong, nothing will blow up, so it's not *that* bad.
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