It's by design that a copy of the project is saved to the temp folder. Think of it as a snapshot of the sequence. Saving these snapshots rather using the "live" project is what allows you to continue editing in Premiere while AME is encoding.
What's not expected is that your main project is being moved to the temp folder. It should remain at the path you specified. Are you absolutely certain that a copy of the project is not in the folder where you originally saved it?
Please try creating a new project, saving it to the default path (/Users/<username>/Documents/Adobe/Premiere Pro/8.0), and exporting to AME. Then check the path shown in Premiere's title bar.