There are some support pages that might be helpful to you:
1 - in Aperture I have clicked the preference to turn Photostream ON, and also clicked the option to Automatic Import. Does this mean that I am both accessing the my Photostream AND making copies of these photos in Aperture at the same time so they won't be lost?
This will import the images from the Photo Stream into a project in the Aperture library. They will stay in the Aperture library, even after removing them from the Photostream.
2 - I see 2 locations for the Photostream pictures: one in the RECENT menu called Photo Stream, the other down below under PROJECTS. If I understand this correctly, the RECENT photos in Photo Stream are just that, the ones in PROJECTS are thecopies on my HD?
I see the Photo Stream in the "WEB" section - this album lets you browse the Photo Stream before importing the images into Aperture, but you cannot edit or tag them. All other mentions of Photo Stream are the projects that get created, when the images are auto imported from the stream.
3 - is it fair to assume then that I have 2 places on my iOS device as well (Camera Roll being ON the device, Photo Stream being in the Cloud)?
The Photo stream is stored in the cloud, and the images are pushed to your camera roll on the device.
4 - it seems that the Photo Stream keeps ALL the pictures I take and doesn't take into account the deleted ones (either on my iOS device or in Aperture), so what happens when I have reached this 1000 picture limit? Is it assumed that since copies are being put onto both my devices (if points above are correct) that I never need to worry about actually losing any photos which I keep?
When you reach the 1000 pictures limit, the oldest pictures in the stream may be deleted. Or pictures older than a month. Make sure you import them on your Mac before the time is up.
The photo stream is automatically added to the camera roll. So it is a good idea to make regular backups of your mobile devices, for everything in the camera roll will be part of the backup, if you backup to iCloud.
5 - finally, is there any way to push only the photos I like (or edit and keep) on my iOS device to the Aperture Photo Stream PROJECT instead of all of the photos? Seems to me that once I connected it all together I found I had to go through and delete all my bad shots a second time, something I would prefer to avoid.
No, not if you use automatic import on your Mac. I import manually, only the images that I want. Or you could ignore the MyPhotostream altogether and create a shared photostream - then selectively add only the images you want to send to your mac to this shared stream. Invite only yourself to view this stream.