1. I can see how to turn on Photo Stream in Aperture but who do I permanenty download the photos? Presumably if I don't permanently download them, the oldest ones would eventually disappear.
They might vanish after a month or if you have reached the 1000 photos limit.
If you set the Preferences for "Photo Stream" to "Automatic Import", your photos will automatically be saved to monthly projects "Feb 2013 Photo Stream" or similar.
You can also drag the photos from the Photo Straem to projects of your choice.
2. How do I permanently delete the photos from my camera roll when downloading from Photo Stream into Aperture? (if I don't do this, then there is a risk I lose track of what I have downloaded and what I haven't).
There is no automatic support for that, but once the photos show in the Photo Stream in Aperture, and you downloaded them from My Photo Stream, you can delete them from the Camera Roll, if you do not want to keep them on the device.
The savest way would be to rely on the automatic import. This way you will not create duplicates or miss something.
Am I able to use the same Apple ID for photos? (I'm guessing not but would clearly help my situation if I can).
You enable the Photo Stream in the iCloud settings with the same Apple ID you are using for other iCloud settings (Mail, Contacts, etc.)
And this AppleID will be used, when you enable Photo Stream in Aperture or iPhoto. That is why you will have to do it from your personal user accounts and have to have a personal Aperture library to be used with Photo Stream.