You restored all files?
That's good.
After installing TB you need to run it.
On the first run TB will ask some questions.
Mail directory? Point it to userdata\thebat, that should be the default
Encrypted message base? Yes!
Master password? The same as it used to be. This is essential, the password is the key to proper decryption.
Restore accounts or create new? New! Enter the same name as you had before. TB will recognize it and use the existing files.
(In case you don't know the exact name, check your mail directory, the account directories have the same name as the matching account)
Back when I was using OTFE (On The Fly Encryption) creating one account was sufficient to restore all of them, but that it's possible that you need to do this for every account.

You mentioned that your accounts weren't recognized, so I guess TB's first run has been done.
In case you picked the proper mail directory and master password, then you continue with creating a new account.
In case you did something wrong, close TB, start Regdit and delete this tree from you registry:
HKEY_CURRENT_USER\Software\RIT
Close Regedit,
Start TB
TB won't see its registry settings and therefore it starts its first run again, continue with the top of my message.