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I do not know if I simply cant wrap my mind around this but...

Do multiple damage causing weapons do damage to multiple models?

For example, if I am shooting space marine primaris with an autocannon. Lets say one primaris was wounded before. I cause 1 wound after the armor saves. Because it is a 2 damage weapon, does that one primaris die and another wounded or does strictly 1 model take all the damage of the weapon even though he does not have enough wounds to take all the left over damage?

One dies really badly. :-)

Damage does not spill from model to model.* In your example, the first Parine would die, and the second would be completely unaffected.

*The exception to this is mortal wounds, which continue through a unit until they are exhausted.

As GW has put it, if a one-wound model dies from a lascannon shot five of his friends don't die from sympathy pains. You've just hit that one model with major overkill.

For a rules reference, this is covered in the last sentence of step 5 in the 'Resolve Attacks' part of the Shooting phase rules:

"If a model loses several wounds from a single attack and is destroyed, any excess damage inflicted by that attack is lost and has no effect."

This rule is modified and roles over only if the damage is mortal

Which opens a Pandora Box that I looked too deeply into once... lets not bring up Mortal Wounds and rolling over "damage" please.
It is still too soon, Tzeentch still has that portion of my mind....

Weapons with more than one Damage (2, 3, D6 etc.) are representing extremely potent single shots. Think a powerful laser beam, or a large caliber shell from an autocannon, or an anti-tank RPG round. They hit one target and do serious damage to it.

A weapon with multiple shots, shown in its weapon type "Heavy D6", "Rapid Fire 2", etc. represents a weapon spraying an area or creating a large explosive blast - inflicting damage on multiple models (or indeed single models if no one else is around).

If you're familiar with historical weapons...consider a light machine gun vs. an anti-tank gun. The light machine gun might mow infantry down (Heavy D6, etc.)...whereas the anti-tank gun would put a clean hole in a single enemy vehicle. Now consider firing the anti-tank gun at an infantry soldier. The anti-tank shell would put a beer-mug sized hole in the soldier and keep going...overkill on a single model.