Ok guys, I am confused as to how a port relates to my armies. For example, Lannister is (2) on the supply track meaning they can support armies of 3, 2, and 2. If I have a ship in Lannisport, do I count it with my land units, or do I count it with my units in The Golden Sea?

We are currently playing as if a port is a seperate area, since they receive thier own orders. So in my example above: I have (2) footmen, and (1) ship in Lannisport. We currently play that I have an army of 2, NOT 3, since I am not counting the ship. Is that correct?

It doesn't mention in the rule book either way. Thanks for your help.

You were playing correctly.

"Ports function as a special area between the land and sea area they connect."

Ports are an area, not part of another area - units in Port get their own orders.

"Multiple Ship units occupying a Port are considered an army and must be in compliance with supply limits."

This means Ships in Port are THEIR OWN army, not part of another army.