INTRODUCTION
Okay one thing thats bugged me since i've been playing dual-box is movement, works fine well you on your main but if he dies or you need to move to your slave things get a bit err, "Confused" shall we say.
So here is my work so far in to solving this problem.

The Goals:
- To Be Able to use WASD on any window
- To Be Able to follow any Toon
- Indepedent casting/assisting of spells (this has been done i know but am adding it for completeness.

NB: If this has been done before let me know.

1. Movement (WASD)
Okay then here is how i've managed this:

firstly ive set up to sets of keymaps for my 2 clients for example

TOON1 KEYMAP FILE
W >>> MOVE.FORWARD.1
LCTRL+1 >>> MOVE.FORWARD.2

TOON2 KEYMAP FILE
W >>> MOVE.FORWARD.2
LCTRL+1 >>> MOVE.FORWARD.1

What does this do?
Well if i press w in one window it send ctrl+w to the other, which by default will make both toon walk forward because of how WoW does hotkeys, so what we need to do is change some keybindings in WOW.
So we need to bind CTRL+W to something in each version of WOW this will stop WOW defaulting to just W being pressed. Since I use Bartender i just use one of bliz's built in acution bars.

once you've done this pressing W will only make your current client walk forward, you could bind a /follow macro to ctrl+w if you wanted which would make the other one auto follow.

I worked through the rest of the WASD keys doing the same for each.

NB: If you hold down ALT and a WASD key BOTH characters will move with that key useful for showing off.

2. Following
Since I dont like auto follow I set up the following in key maps

TOON1 KEYMAP FILE
G >>> FOLLOW.TOON1
LCTRL+G >>> FOLLOW.TOON2

TOON2 KEYMAP FILE
G >>> FOLLOW.TOON2
LCTRL+G >>> FOLLOW.TOON1

In Wow i then bound my follow macro to CTRL+G on each toon.
NB: If your so inclined you can set something up on your main to emote "Follow Me" or something on G anoys the crap out of people and kinda looks good.