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JeremyS, it depends on the case. Generally speaking, an AMD cooler has to be put on with the aid of a screwdriver. In a lot of case/mobo situations, the case or the PSU tend to be in the way. In such a case, the processor and cooler are easier to install *before* putting the mobo into the case. Since this wouldn't add any danger/problem whatsoever, I suggest you do the following:
1) test-fit the mobo into the case, add risers where appropriate (8 to 10 in total should suffice)
2) remove mobo from case, install CPU and cooler (remember to check the orientation; there's a ridge on the socket, and an extrusion on the cooler.)
3) install the mobo into the case with the stuff pre-mounted.
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