In most jurisdictions' workflows, fees must be assessed and paid before a permit can be issued. In most workflows, when you update the status on a Permit Issuance step, you will be reminded to assess and take payment on fees first.
How to assess fees
In the permit, click Fees, then the Actions button dropdown, and select Assess Fees.
Select the fee(s) you need to assess
Enter payment after assessing fees
After assessing fees, you are given the option to enter a payment now or return to fees and enter a payment later.