Partial Payments

We partially paid some invoices wanting only to pay a certain project's amounts. However, FENXT only allows you to enter an amount by which FENXT distributes the way they want the payment distributed. I wish there was a way that we, the customer, could tell FENXT how we want the payment distributed by being able to check the line item within the distribution of the invoice. Now it is causing one of my projects to look overdrawn even though it is not.