I use PkgBackup in Cydia. It's always worked well for me and it's great now that you can save your backup in two places...as a contact (you just have to remember to sync your contacts before restoring) and you can save a copy to Dropbox.
*edit* After rereading your post, are you talking about adding packages via SSH or directly from Cydia? I'm not certain (maybe someone that is can chime in and help out), but I'm not sure PkgBackup will back up your SSH'd-in packages. THAT would be a good question.