You can add a payment three different ways within the app.
First Option, navigate to Money on the lower navigation pane shown below.
Second Option, tap the blue circle "+", then tap "Income".
Third Option, go to your Pupils >> Select Pupil >> Payments >> Add.
Here you can now add a payment, the date, the reason, assign the payment against an active pupil and opt to send the pupil a receipt, if you don't want to do this, uncheck the "Send email payment receipt to pupil".
Once finished, tap save.