Huh? Manual Check and Payment Entry is a function in AP, the PrePayment stuff you are talking about is a function of Cash Receipt Entry in AR.  In your post you are combining functions of AP and AR.

Now if you mean you are entering a PrePayment in Cash Receipt then when you invoice you MUST use the same invoice number for the system to apply one to the other. If you do not then you must do a zero dollar cash receipt and apply one to the other.

Also do you mean that on the totals tab of the sales order you are again entering the deposit amount? Don't do that if you have a PrePayment on their record.

Yes, you're right - I meant Cash Receipt entry.  We are using the same invoice number when generating the invoice from the Sales Order and the PP and IN are matching up.  But, I am also entering it on the Totals tab of the Sales Order, which appears to be creating my issue.  

Any known way to remove the extra PrePayment from the Customer's account?

I went to the doctor once. I told him it hurt when I hit myself with a hammer and he told me not to hit myself with a hammer.

If entering the amount on the Totals tab of the Sales Order is the cause of your problem I sure hope you are not continuing to do it.

To remove you have to do a zero dollar cash receipt and select the PrePayment.

I have stopped adding the deposit amounts on the totals tab of the Sales Order and it is working like a charm.

But, I still have 2 instances that I need to clean up.  I tried doing a zero dollar cash receipt, but I think I'm miss a step because it is either out of balance or just shows up as a zero payment.  I'm sure I'm missing something obvious, but if you could provide some more details as to what amounts should be listed on the entry, it would be much appreciated.

To clear a prepayment, you must do a negative cash receipt entry.  If your prepayment is for $100.00 then through cash receipt entry:

• Make your cash deposit amount  -100.00, click accept.
• Put in the customer number
• Put something in the "check number" field. Such as CLR PP
• Put -100.00 in the amount received field.
• go to tab two.
• pull up the prepayment, and hit accept.

When you post, this will eliminate the prepayment, and remove the excess money from your cash account.

If you do a zero value cash receipt, then you must chose the offsetting GL account in the secondary grid of tab two. (lower left, where it say's line type "invoice", use the drop down arrow to change to "GL Account" and then put in the account number in the space below).

Entries made to a GL account this way will be a debit if the line item is negative, and a credit if the line item is positive.

Hope this helps.

Thank you for the reply.  I think I'm almost there with this solution - but see that the negative receipt is now showing up in my Bank Rec as a Deposit.  

You should have done a zero cash receipt and selected the prepayment and cleared it and then did a GL distribution to the GL account you setup for Customer Deposits (Sales Order - Setup - Sales Order Options - Main Tab).

Joe