That's right, when you're using OTFE (either with Voyager or TB) the encrypted files have the same extension, but the first character of the extension is always an E. So you'll see different file names.
You can only exchange the files between TB and Voyager when both are using the same master password (as the password is the encryption/decryption key)
The only way to exchange quick templates between TB and voyager is by copy and paste. However, you can run TB and Voyager simultaneously on the same computer, so the copy/paste is rather straightforward.
I'm just a user of The Bat! I don't work for Ritlabs.