Install the CPU/heatsink before mobo in is case?

You install the CPU and mount the heatsink before you put the motherboard in the case. In smaller cases you may not have the clearance neccesary to install the heatsink after the board is installed in the case. Additionally, the screws/clips/etc. of the heatsink are more accessible when the motherboard is outside of the case.

Always remove existing thermal material (Artic Silver) and apply a fresh coat when you remove the heatsink.

I don't think you followed. It's a brand new motherboard, Opteron, and heatsink/fan. The heatsink already has a fresh coat of thermal paste from the factory.

That's what Mex meant. That coat of thermal paste from the factory should be removed before applying Artic Silver. If you remove the heatsink for any reason, it's always better to clean the heatsink and apply a new coat of thermal paste.

Oh, and yes, it's much easier to install the heatsink/cpu when the mobo is out of the case. Especially if you have to use a backplane clip or need to tighten stuff from behind the motherboard.

I didn't mean to be so vague; I didn't realize you were talking about a heatsink with paste pre-applied. The stuff on the heatsink will do the job, but Artic Silver is better - if you have AS, I would go ahead and use it, especially if you plan to overclock.

Cool. And I just follow the instructions on their website, one rice sized dab and apply the heatsink? I don't have to smear it all over or anything?

I think it depends on your CPU. The site has you choose your CPU, and for an Intel dual core it has a thin line run down the CPU instead of the dot.

You are doing it the same way most experienced builders do.
The idea with any thermal paste is to get the least "usable" amount down. Any extra is actually bad. You want a layer that is transparent, that's all.
The purpose of thermal compound is to fill the small cracks and wholes, to keep air out.
A mating surface of metal conducts heat away, much better than any paste can. This requires a flawless lap on bothe hs and heat spreader, which I do not recommend. A wee bit of AS can fill the flaws, without too much loss of thermal conductivity. You should not use more than is needed to fill those flaws.
A grain or rice is larger than the amount of AS that is used by most experienced builders.

From the Arctic Silver installation .pdf:

Understand that we are just putting thermal compound in close proximity to the center of the heatspreader. Only a small amount of Arctic Silver is needed. The example at left shows you an approximate amount to use, about the size of one and a half uncooked grains of short-grain white rice or ¾ of a BB.

I guess I should have specified uncooked short-grain white rice lol. Do you agree with the instructions above?

I've read all about the purpose of thermal compound, lapping, and installation but I'm feeling apprehensive as I've never done this before.

Thanks, I just put it on. Now for the RAM, HDDs, case etc.