How do configure Aperture to permanently adjust my original file, and keep only that one?
Can't do it. The philosophy behind Aperture is non-destructive editing of the original. The original master is never modified. The versions you create are actually instructions to Aperture telling ti how to create the modified image from the master. No actual image file is created until you export that version. The size of the version instruction files are really very small in comparison to the original master file.
I want it to be a permanent adjustment and I do not want to keep the original.
The adjustment you make to create a version are permanent, no worries there, Not wanting to keep the original is going to be a problem if you use Aperture. As I said above the whole point of Aperture is to preserve the original. You would have to export the version, delete the master (which will delete all versions associated with the master) and then (if you still want to use Aperture, but not sure why you would at this point) import the exported version back in.
Any metadata you applied to the version, ratings, faces, places will be lost, you will have to reapply those if you want them on the new 'master'.
cropped a photo and when I went to export it, it exported the original.
Sounds like you exported the master rather then the version you created with the crop. If you modify a master you need to export the version you created.
Here is the short version of Frank's excellent answer (which you should go through step-by-step and make sure you understand all the steps):
Aperture works well as is. You exported the Master when you wanted to export the Version. On export, you can specify the image format, size, and other parameters of the file(s) you are creating.
I cropped a photo and when I went to export it, it exported the original.
This was a simple (we all did it at least once) user error. Correcting the error requires no change in how Aperture is set up.
I posted a concise guide to the parts of Aperture and how to get started with them; you may find it helpful.