It's not clear exactly what you did.
What version of OSX are you running now, and what version is on your backups?
In most cases, all you need to do is restore your most recent TM backup, per Time Machine - Frequently Asked Question #14. That will, however, revert to the backed-up version of OSX.
How did you change the software version? If you just installed, say, Snow Leopard on the empty drive, and have done nothing else, you should be able to use Setup Assistant to transfer your apps, user accounts, and data from the backups, per Using Setup Assistant on Snow Leopard or Leopard, unless the latest backup was made on Lion.