It's really up to you, some decant, or some just swirl it all in. It like so many things is really a matter of choice, more than anything else.
One factor to consider is whether or not the "starter beer," the liguid on top smells sour or not. Often, especially in the summer it may sour in only a few hours. Some folks add a hop pellet as a preservative/preventative measure. The couple of ounces of sour beer wont really affect the taste of your finished product (unless maybe you were brewing an extremely light tasting beer.) It's really up to you.
Another factor is whether or not the yeast is a low flocculating yeast and there may be a lot still in suspension. The "beer" will be cloudy rather than clear-ish. If it's a witbier or hefe yeast for example it might be better just to swirl and pour it all in, you'll get the max number of yeast cells that way.
My starter flask is huge and often I will build up a starter over a few days and end up with 1 1/2 to 2 quarts of "beer" in it. If the yeast has pretty much flocculated I will, if I have time cold crash it, but even if I don't I will carefully pour off all but about 2 cups of the liquid, then swirl the remainder to re-suspend the yeast and dump it in my fermenter.
Like my snazzy new avatar? Get Sons of Zymurgy swag, here, and brew with the best.
Revvy's one of the cool reverends. He has a Harley and a t-shirt that says on the back "If you can read this, the bitch was Raptured. - Madman
I gotta tell ya, just between us girls, that Revvy is HOT. Very tall, gorgeous grey hair and a terrific smile. He's very good looking in person, with a charismatic personality... he drives like a ****ing maniac! - YooperBrew