How can I migrate apps without a bootable backup drive?

I recently had to reinstall OS X because my MacBook Pro had slowed to a crawl.

The good thing: Now the OS works fine.

The bad thing: I was using an external drive with ProSoft's Data Backup to protect my files, but now I can't figure out how to migrate them into the new OS. Migration assistant doesn't recognize them. And I just did simple backups as opposed to creating a bootable clone.

Any thoughts on how I can get my data back onto my internal drive without having to manually add program after program, and individual pref/app files?

Thanks.