If you want to have a good back up connect you firewire drive, then when formating the drives using disc utilities create a ride format using the mirrow option. That way you will have just one drive ico in your desktop but what ever you are doing is going to clone to your external drive as well. In that case if you loose one you will have an exact copy of everything in the other drive.
Now, if you want to have the external drive as it is just run everything from your internal drive and keep files in the external. That is what I do, video files are outside and pictures, softwares and music inside.