Yes. The stamp duty you are paying during your application for registration is premised on the share capital of the company you seek to register.
For the calculation; it is usually approximately 1 percent (one) of the total share capital amount you are registering.
For the payment; you can pay directly while doing your registration. You could be redirected to the Remitta Portal which is quicker and instant and a remita receipt woudl be sent to your email with an RRR
Conclusion; after payment, FIRS would send you an email and you should follow that link to setup your onlie profile, finalise your transaction, print your payment "certificate" and get your personal TIN free.