Atoms may, at times carry a charge. But, as experiments with early atom smashers have found (and we're still working on it -- go CERN,) atoms are not "made up of charges" no can you take a hydrogen nucleus, basically a single positively charged proton and separate it into "a positive charge" and "something else," like you imply. That's pretty much the maximum extent of my knowledge on the subject*, but I just wanted to help you though the thought process and terminology.
*Well, I am aware that protons and neutrons are made of quarks, and the quarks themselves have states, but there's no quark that carries the entire positive or negative charge. But yet, not fractional charges either. But then the topic gets muddy, at least for me.