You have to make a major decision now. You can "pilot" via Focus ... or you can use Focus for CC. I chose to "Pilot" via Focus. What this means is that every toon I have sets my Main (a prot pally) as their focus. All spells are then based on focus.

Fireblast for example:

Code:
#showtooltip Fire Blast /cast [target=focustarget, harm][target=targettarget, harm][harm]Fire Blast
All of my harmful spells are configured this way.

CC on the other hand, works a little differently:

On my Paladin I have F9-F12 bound to assigning Raid Icons. On each of my 4 alts I have this:

Code:
#showtooltip Polymorph 
/target focustarget 
/cleartarget [target=focustarget,noexists] 
/stopmacro [nocombat] 
/stopcasting 
/cast [target=focustarget,harm,nodead,exists] Polymorph
If I am out of combat, it sets the Target of my Alt to the mob that it will CC. Since it will cast harmful spells at the target of the Focus first, they will ignore this guy. If I am IN combat, and I hit this, it is usually because I got an add - so I hit this button and it marks the target and CC's them with 1 button press.