On the liveries that you can download from the PMDG website, After you install the livery Are the settings in the aircraft airline specific, Like you did with deliveries in the 777? Or is there like a way to download for example certain settings that are equipped in the Alaska Airlines fleet?

ones with settings are denoted, by asterisk I think.

So when I Download one with the red * that one has Company settings? So every time I lode it it will lode those settings?

Yes.