If you fly for Skywest - you are hired by them - you will wear a Skywest uniform. You will fly Skywest airplanes. You will get paid by Skywest.

I used to work for United at JAX. All of United's flights into and out of JAX are operated by Air Wisconsin. So, Air Wisconsin pilots would come in and get on their Air Wisconsin CRJ's (that say Air Wisconsin on the front and have a great big blue and white "U" on the back for United). It's not that the pilot's are flying for United, they fly for Air Wisconsin - Air Wisconsin flies for United in JAX.

I think that you may be making it more complicated than it is. Just apply where you want to go, they'll tell you what airline they're flying for that day.