If an employee no longer works for me, do they still count toward the total employees that I would be paying for?

No, when an employee no longer works for you, you can either de-activate the employee (which still saves all their data), or delete them from the system. Either way, they do not count as an employee in terms of billing. If de-activate them, you can still access all their data, and even re-activate them later, but we do not charge you if they are de-activated.