The same way you optimize a neutral molecule. One problem you may encounter is that usually Zwiterions are not stable in gas phase, so the optimization goes back to the neutral form. In that case you may need to simulate the media to stabilize it. A typical example is glycine, which in gas phase exists as neutral, but in solution the Zwitterion form is more stable.
You cannot do that. The charges are calculated from the electronic density after the SCF is performed. There are several methods to calculate charges on a given atom, but this is a different story.
Glycine has proton transfer, so it can be zwitterion. Localizing charge cannot reproduce a zwitterion. And zwitterion can be stable under the influence of polar group like metal ion and water.
If you follow what Saman has stated and then optimize the geometry in a polarized medium (e.g. PCM keyword in gaussian with the choice of your solvent) it should avoid the neutralization which is bound to happen as Saman and Antonio have already stated if you optimize in the gas phase.
A possible solution can be constrained DFT, where you can localize the charge or spin density in different parts of your system. It is implemented in NWChem and Q-Chem.