Motherboards in general are not hard to replace, but it might be scary for a first-timer. If you don't get the exact same motherboard, there is a chance that the computer will have to be formatted (hard drive erased) for the new motherboard to work. Motherboards come in three formats: ATX, Micro-ATX, and Nano-ATX. Chances are your e-machines motherboard has an ATX motherboard, or a Micro-ATX motherboard if the machine is smaller than most computers (physically). Other motherboards will most likely work with it, but you'll need to buy one that is compatible with your processor and RAM.
I'd just buy the e-machines motherboard if you feel like you and another person can get it installed properly. Most motherboards are $70-$150, so it's not that bad of a deal. Can't Best Buy install it for you? I'd try to get that arranged if you've never installed a motherboard before.
*EDIT* I assume the $300-$400 is based around labor also. That's not a bad deal, because store-bought computers can be rough concerning motherboard installation unless you've did it multiple times.
-Lasereth
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"A Darwinian attacks his theory, seeking to find flaws. An ID believer defends his theory, seeking to conceal flaws." -Roger Ebert
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