I bought my own application from the Mac AppStore. The app was not saved in the Applications folder, but instead in /Users/nathan/Library/Developer/Xcode/Archives/2011-06-14/Release PackageTracking 6-14-11 12.09 PM.xcarchive/Products/Users/nathan
Is it just for me because I am the developer? Or are all my users going to have to hunt down that file? Why didn’t it download it to the correct location?
You have to find and delete (or hide) absolutely every copy of your application (all debug copies, archive copies, anything with the same bundle ID) from your system before doing a test purchase.
You can try using Spotlight to find apps.
One way to hide apps is to compress them using gzip. Or move them to a disk drive that can be unmounted.
Users with no previous copies of your app won’t have this problem. Users who have previous copies of your app and who put these copies in strange places might encounter this problem.