When you receive payment for an invoice, you can mark it as paid in a few taps: Invoice tab > Tap the relevant unpaid invoice > Tap the three dots in the top right corner and then scroll down to 'Mark as Paid'.
Why can't I mark a draft invoice as paid?
A draft invoice is an invoice that hasn't yet been sent yet, as such it would make sense that payment would not have been made yet. If, however, your client has paid you without you sending them the invoice, a workaround would be to send the invoice to yourself so it shows as being sent in the app, and then mark it as paid. This will keep your invoice view current.
Read more:
Automatic matching of your invoice payments (and how to mark invoices as paid)
Manage your invoices (see which invoices you've got paid, unpaid, late or unsent)