We all make mistakes, it's life.
PkgBackup is a very good Cydia App. When I updated to 4.2.1 from 4.1 my backup through PkgBackup was corrupt, I lost everything I had previously had. I wish I knew about the Dropbox feature...
Aptbackup I've not personally ever used, it had mixed ratings so I went for PkgBackup instead.
At least you've finally got everything sorted, that's the main thing
