Trados Business Manager has a mechanism of partial payments over invoices.

To add a payment, select Payments on the Workspace group of the navigation tree. Click New or Clone buttons to start creating a new payment.

Then, fill the details of the Payment document. Start from specifying a client and amount. Then, if you amount actually received is less than instructed amount, specify bank charges (bank fee). This amount will be accounted as expenses. Also, if payment currency differs from your base currency, you can specify currency rate used to recalculate payment amount into amount in your base currency. Currency rate field contains Refresh button (to re-detect currency rate from currency rates list) and Download rates button (to download new rates).

When done, you can start edit details table. This table allows to link the payment with invoices. You can manually select invoices or use Add invoice(s) button to select from available unpaid invoices. You can add one invoice (if this payment is made against one invoice) or multiple invoices. In the Amount column of this table you specify an amount (part of full payment amount) which should be assigned for a selected invoice. If invoice is not paid in full, you will see that in the list of invoices. The invoice and corresponding jobs will be marked as paid only when paid amount will correspond to invoice amount.