Hi Liz, normally the time you wonder whether or not you should stir in the hooch comes when you go to feed it, and if you're feeding fairly regularly and consistently (in terms of the balance of starter/water/flour) then you shouldn't have to worry about the hooch affecting the starter adversely. The times you might end up with a very sluggish starter are if you routinely add just a little flour and water to a large container of starter without discarding any of the starter (which won't provide adequate nourishment), or if you leave your starter in the refrigerator for a very long time without feeding it. Neither situation is likely to kill your starter, but it might result in a starter that seems very slow and unresponsive at first. Usually a few days of twice a day feedings at room temperature according to our feeding routine will restore your starter back to its normal rising behavior and aroma. During this revival period, try to feed the starter when it's ripe (at it's highest point of rising, or just beginning to fall) rather than after it has fallen significantly. Feeding your starter when it's ripe will help to keep the yeast active and vigorous. 

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