Honestly, you seem like you are WAY overfeeding (Don't worry-I've been there before!) Her being only 4 1/2lbs.... my 15lb boy eats the same amount each day (1/4 cup in AM, and 1/4 cup in PM) along with a bit of wet food and some treats during the day. That would totally explain why she's pooping so much. I feed Acana mainly but have also fed Go! Endurance (makers of Now!) and the bag states a 50lb dog should be fed 1.75-2cups per day for reference.
You've gotta remember that with higher quality, grain-free foods, often times you feed a lot less.
It is a more rich food than others and it's sooo easy to over-feed. On a few other forums I belong to, people often state that even if they barely overfeed some of the better foods, they can notice in their stools that it is too soft, etc. So I really think I would just cut back her food!
Btw, yay for another Maryland'er! I'm in Annapolis area. Have a few step relatives in Frederick area, and we often visit to Charlestown, WV, etc which is close-ish to there.