Charles n'est pas ici?
This is correct, but we would say "là" instead of "ici", which is smoother.
Note there is a "liaison" on the "s" of "pas" before "ici".
N'est pas elle là
Indeed, this is not correct, you should say:
N'est-elle pas là ?
NotNote there is a "liaison" on the "t" of "est".