I'll certainly try to walk you through the steps here to get this sorted for you.
The first thing to do is to record the transaction in full and record it against the supplier. So, I'll go through a quick example of a £1,000 payment made for a £400 invoice, with the rest held on account.
Start by clicking 'Tag me!', and then selecting 'Payment to supplier':
Unless you have other invoices for the same value in the same date range, you'll see no matching purchases. Click on the 'Pay down multiple invoices' option:
Then enter the name of your supplier, and select them from the list. Select any invoices this applies to, and click save:
If you were to click on the 'Tagged' button again, it would show that it's unallocated. However the full amount is now assigned to that supplier, and can be seen in their overview:
When it comes to paying a different invoice, use the 'Log Payment' button and pay from credit:
You can use that option until the credit runs out.
Hope that helps!