When any carrier hires you, you bid on position, equipment and crew base in a preferential order. The actual carrier you are feeding for (ie. United, Delta, American, etc...) really doesn't matter. Usually, the crew base determines which carrier you are feeding for, but not always.

You'll wear a specific uniform from the company that hired you (ie. Skywest) and fly one aircraft type, regardless of which airline that feeds for. That means that you may fly two legs, feeding for different companies, but your are stil flying for your company. Many times the flight itself has multiple flight numbers (for passengers) depending on through which airline the passenger bought a ticket through. All in all, I wouldn't worry about it too much.

What is nice is that you usually have nonrevenue flying privileges on ALL the airlines your company feeds for, even if you do not fly those routes yourself.

When you submit a bid as a new hire, make sure your bid reflects the equipment, base and positions you prefer- NOT which airline it feeds for.

Hope this helps.