Partially paid invoice

I have a client who is booking accommodation on behalf of their client and requests that we invoice for the gross amount which includes their commission. This i have done, however they deduct their commission when making payment in respect of the invoice. I created a journal entry in respect of the commission to credit the debtors account. This obviously balanced the debtors account but still left the amount outstanding on the invoice. How do i receive payment for the commission element of the invoice to clear the outstanding amount?

Thanks