The “feature overlap” exists so each program can stand alone in addition to being tightly integrated. As far as what app to use for each job is simply a matter of preference since you have the whole Studio. I really like how Homesite 5 is also part of the package (look through the CD files and folders if you weren’t aware of this) and integrates into the package as well. Although I usually prefer working with Xara-X over Freehand, the perspective grid feature of Freehand Kicks some serious Butt!
There are a whole load of tutorials for each of the programs scattered all over the net, hunt them down and you’ll find features in the programs you thought weren’t there. I guess what I mean to say by that is at first glance (Fireworks for example) looks feature poor, truth is I hardly even open Photoshop any more because I can do so much in Fireworks. It also loads faster and isn’t even close to being as much as a memory hog (don’t get me wrong, I still love Photoshop!).
Don’t know if any of this is what you were looking for, just tossing my two cents in at 2:15 am. I still think Macromedia MX Studio is the best software money can buy. I use the Crap out of mine!

Jeff