Overpaying a line in AR Advanced Billling

We had some turn over in our accounting department - hence - all the questions.

In the Advanced Billing, you need to do this by line.

The whole amount was applied against the first line.

When it shipped it with the 5 other lines - well - it went only to line one.

Now we have a Advanced Billing on the Sales Orders but, when I do the Advanced Billing Credit Memo - it is going to Sales Income and AR accounts - not our Advanced Billing account.

Does anyone know how to fix this?