You will have to click on 'find and match' in the reconcile screen and select the invoice. Towards the right of the screen, a blue 'split' link will appear. You can click on this and reconcile the part payment. If you go to the invoice you'll notice the part payment that has been matched with the balance owing. Click here to find out more.
If you have any questions please contact your RightWay accountant, email firstname.lastname@example.org or call 0800 555 024