hate to say it, but this is common with formula. stool will happen less frequently, since formula is MUCH more concentrated than breastmilk. it can also cause constipation (which isnt the lack of stool, but a hard, painful passing of stool)
regardless of what people may tell you, water is safe, and healthy for babies. if you are worried about what is in the water, you can use a water filter system of some kind; britta or pur something like that... if you have well water, there is probably little to worry about. after all, you are using that water to make the formula, so even if you have city water and are using it for formula, its sillly to think that it will harm her to give it to her plain... just make sure that you always have fed her first, and make sure you never give water to replace a feeding... always use it to "wash it down" or something you know? she wont ever take too much if shes already full, and it really doesnt take much water anyway to help a baby's system, so dont worry about giving her any specific amount. even a teaspoon or tablespoon might be plenty.
if constipation is an issue (remember its hard stool, painful to pass, difficult to pass, not the absence of stool) when she is older and starting solids it is perfectly healthy and normal to add milled flax to her cereal. some people may think that this is somehow harmful, or that your body will then NEED the flax to pass stool... but its not harmful, after all, its not a drug, flax is just fiber, which we all need to maintain healthy stool. fiber absorbs water and passes right through the intestines, keeping stool soft. so its a good thing. and it doesnt take much flax either... you can even use it yourself if you have an issue with that... a teaspoon or so at first for an adult (which gives you an idea that a tiny tiny pinch is probably good enough for a baby...)
ive even used flax in babys formula, but it does sometimes block up the nipple, so its not the easiest way to do it...
anyway...
pump her legs when shes fussy or trying to poop, massage her tummy during that time also, give her a bath (i know, asking for trouble, but warmth helps sometimes)even a warm towel on her tummy...... that kind of thing.
they have that mylecon stuff for gas, always worked like a charm with my son. also check out a health foods store for any natural type additions to her diet. they might have something that you can use that is not harmful and will be easy to make her comfortable.
good luck! :D