I've just recently started dual-boxing with the release of TBC and have been having a ton of fun with it since finding this site and MultiBox.

I'm running two boxes at once, levelling my warlock and hunter. The only special software I'm using is MultiBox, thought I, too, am using a Nostromo n52 gamepad.

I've spend most of my time trying to synch main combat button presses between my two characters. When I first start the group with my warlock as the main, I set my hunter's focus to the warlock and set him to follow. I've unbound the movement keys on my hunter so I can keep keyboard broadcasting active most of the time and that's helped a lot in combat. My typical sequence is:
[code:1]
Button 1: warlock: activate trinket for damage boost (otherwise I hardly use it)
hunter: macro : /target focustarget; cast Hunter's Mark.

Shift-1: sends both pets to attack target.

Button 2: warlock: cast shadowbolt
hunter: macro: /castsequence reset=6 Arcane Shot,Steady Shot,Steady Shot,Steady Shot;

Button 3: warlock: cast curse of agony
hunter: cast serpent sting

Button 4: warlock: cast corruption
hunter: cast rapid fire

Button 5: warlock: cast drain life
hunter: cast Multi-shot
[/code:1]

In typical fights I mostly just use 1,shift-1,2,2 and by then any single non-elite target is dead. I typically run with the warlock's Felguard out as "tank" and the hunters' full-BM enhanced Ravager set for DPS. I'm getting better at fighting multiple targets at the same time, but if I forget to sat the hunter's pet to autocast Growl, the hunter pulls aggro and something gets close I usually have to take care of it with the warlock.