You do have the option to partially pay an invoice within the Fidesic Customer Account Center
From Pay Invoices
From the Pay Invoices page you have the ability to partially pay invoices. Once you've selected the invoices you'd like to pay, the amount becomes editable, and you can change this amount to be a partial payment amount.
From Individual Invoices
When you click pay on an individual invoice, you have the option to change the amount on the Authorize Prompt. To Partially pay, change this amount and pay as normal.