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Ideally, a nonzero formal charge should be located on the outer atoms rather than the central atom. If there's no way of avoiding a formal charge on the central atom, it should be the smallest nonzero formal charge out of all the atoms in the compound.
If it is not possible for all atoms to have a zero formal charge, make sure that atoms (like oxygen) that are more electronegative have a negative charge. An atom like oxygen should never have a positive formal charge; it would never exist in that state.
It does matter what formal charges the atoms have because you are always looking for the most ideal/stable structure. In general, more electronegative atoms should have negative formal charges as opposed to less electronegative ones. Granted, you would want them all to be zero ideally, but if the overall charge of the molecule is say -1 and you have [BrO3]-, O is more electronegative than Br so you would want it to have a negative formal charge, not Br, while keeping all of the other atoms at 0 or as close to 0 as possible.
Negative charge should be on the more electronegative atom such as oxygen and positive charge should be on the less electronegative atom. However this comes seconds to filling up octets or getting the overall charge to 0.
There are multiple structures that will get you the same, correct overall charge. Thus, you want the structure that has the most 0 formal charges as possible (because this ensures the most stability). If there is a negative formal charge on an atom, it should be on the most electronegative atoms (like oxygen is more likely to have a negative formal charge than carbon is).
Yes, it matters. The most ideal situation is to have 0 formal charges on each atom. If it cannot be 0, then it is best to have the least absolute sum value of formal charges with the most negative on the most electronegative element.
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