Hi Titus, yes, if you're measuring by cups then you always want to stir down the starter before measuring and feeding. When measuring by weight, it isn't necessary to stir it down, and by the time you add the water and flour there will be more than enough stirring involved. As far as the dark brown liquid goes, this is a sign of a very neglected starter and isn't anything you want or need to achieve, although you may run into it down the line if you leave your mature starter in the back of the refrigerator for an extended time. 

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