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If I buy an upgrade of Aperture from Apple's online store will they emails me a serial to unlock the trial version and send me a box or just send me a box?

Depends which option you choose: If you choose the serial number only, then you get a serial number straight away but no boxed product. If you choose the boxed product you get that sent to you but no immediate serial number. There's no option to get both (presumably because the boxed product is produced with a serial number inside and they don't know what it will be until it's shipped)
 
Does anyone know if you download Aperture 2.0 and elect not to get a box shipped to you do you also get the manual in PDF format?
 
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