Raider,
I suggest you study plenty of photos. Many are available at the US Navy Visual News website www.news.navy.mil.
In general, all Nimitz-class ships weather in a similar fashion. There's little weathering on the island itself. Most islands are maintained well during a deployment. The only noticable weathering, at scale, would normally be some smoke stains on the forward port side. This occurs when E-2C Hawkeyes start engines while parked up close.
Photos will show you where rust and an overall light gray streaking occurs along the hull. This can be light or heavy depending on how you want to represent the ship.
The flight deck takes the most work. Even with freshly painted stripes, the non-skid surface will be in 2-3 different shades. This stuff fades very quickly in sunlight and rarely goes down all at once. You can even show fading with sharp edges, since one section of deck was coated to definite stopping spot.
I'm not sure how you normally do your weathering, dry brushing, washes, air brush, etc.
I'm sure if you ask more detailed questions, you'll get lots of help.
Photos are the way to go.
Mike