If you don't want to pay an invoice in full right now, you can pay part of it and settle the rest later.
How to make a partial payment
Go to Bills and select the invoice(s) you'd like to pay
Click Pay
On the review screen, edit the amount next to the bill you want to partially pay
Complete the payment as usual
What happens to the remaining balance
After a partial payment, the invoice stays in your Bills section with the outstanding balance. When you're ready to pay the rest, select the same invoice and pay the remaining amount, or make another partial payment.
Splitting a bank transfer into multiple payments
If you're paying via bank transfer and your bank has per-transfer or daily limits, you can send the total across multiple transfers using the same reference. Apron waits for the full amount before processing. See Pay via bank transfer for details.