You've got the right idea; you can edit the script in notepad or any other text editor, and if Crypt::Blowfish_PP is designed to be a drop-in replacement for Crypt::Blowfish, you should be able to make the changes you describe. Whether it will work perfectly or not will require you to try it and test it.

There's no real way to make the key invisible in the program, since the program needs the key. You can take various measures to obfuscate it, but they can all be figured out by anybody with a little perl knowledge. You can protect it with OS-level protection, like file permissions controlling who can see and run the script.