Please go to Tenant Manager => Payments => Choose the tab (either Tenant to Landlord or Tenant to Letting Agent) => Click on Add Payment.
Select the tenant, date and enter the amount of the first payment. Complete the rest of the details. The partial payment will be assign to the invoice (if you have more than one invoice created at this time, you may need to check that the payment has been assigned to the correct invoice (you can delete the amount in the "Amount Allocated" column and re-enter it against any of the invoices)).
Now repeat the process, this time entering the amount of the second payment that you recevied later in the month. The invoice should appear again in the list below since it was only partially paid the first time. Again, if you have more than one invoice created, make sure that it's assigned to the correct invoice.