Let's take a first level character with a dagger.
He can take the attack action, in which case he can either stab with the dagger, or throw the dagger. Or he can take the full attack action, in which case he can either stab with the dagger, or throw the dagger.
Now let's give him the Rapid Shot feat.
He can take the attack action, in which case he can either stab with the dagger, or throw the dagger. Or he can take the full attack action, in which case he can either a/ stab with the dagger or throw the dagger, or b/ use Rapid Shot, taking a -2 penalty on all attacks, in which case he can stab with the dagger and throw the dagger, or throw two daggers (assuming he has them drawn or has Quick Draw).
Now let's give him a dagger in each hand.
His attack action is the same as always - stab with one dagger, or throw one dagger. Only one attack with an attack action.
His Full Attack action, he has numerous options. He can make a melee or ranged attack with his primary dagger. He can make a melee or ranged attack with his off-hand dagger. And he can also make a single extra ranged attack via Rapid Shot with one dagger (could be either dagger). Assorted penalties apply: -2 to all attacks if he uses Rapid Shot; -2/-2 if he is wielding both daggers and has TWF; -4/-8 if he is wielding both daggers and doesn't have TWF.
Now let's give him a BAB of +6 and the ITWF feat.
He gets two primary attacks, and two off-hand attacks, and one extra ranged attack. So he could make four melee attacks and one ranged attack, or five ranged attacks (assuming he has five daggers and the Quick Draw feat), or anything in between. Or he can only make four attacks and not suffer the Rapid Shot penalty.
Now substitute all those daggers for waraxes, and the same applies as long as he has the feat or the enchanted axes to let them count as ranged weapons.
Rapid Shot is an option you have if you are taking the Full Attack action, not a separate Full Attack action in its own right - does that make sense?
-Hyp.