You are correct in saying that
1 17 S
would just indicate that you have a
Cl atom but with an
NetCharge flag. If you look at SIESTA's user guide it explains what it does. However, then you'd probably be defining a periodically charged system. Does this make sense? You should read carefully the indications in the manual to know if your system fits the very specific requirements for it to work.
A more natural thing is usually to have a neutral system where your atoms get naturally charged because of the positions of their energy levels. Say if you think there's a $S^-$ in your system, there probably is a positive ion as well that is donating the charge.
You can then check Hirshfeld, Voronoi or Mulliken charges to understand if the atom is really getting charged. SIESTA will give you these outputs with the flags
WriteMullikenPop, respectively. You can then check your output file manually or color your structure with charge values using
sisl, for example (in python):
# Get your structure
geom = sisl.get_sile("myfile.fdf").read_geometry(output=True)
# Get the last charges from the output file
net_charges = sisl.get_sile("myfile.out").read_charge(
"hirshfeld", iscf=None, imd=None, as_dataframe=True
# And plot the structure using the net charges as the color for the atoms