Yes, you can pay your bill partially by filling a partial amount in the Amount Received field.
Steps for the same is as follows:

1. Click on the desired unpaid Customer Name (whose dues are unpaid).
2. Click on the Record Payment button, on the Invoice Info page.
3. Fill the amount you want to pay in the Amount Received field.
4. Click Submit.
5. Payment Receipt will be generated,  and in Invoices page, the status will be changed to Partially Paid.