What do the Photo Stream settings in Aperture do?
Automatic Import: Imports any pictures received via Photo Stream into the main Aperture library. A copy will be created for this which remains even after the 1000th picture has been added to the stream and which can be edited
For this to work Aperture has to be open/running. If the 1000 picture threshold is reached while Aperture is not running, pictures will get lost irregardless of the setting of this option.

Automatic Upload: Push any picture created in Aperture into the Photo Stream and on to all other connected devices