Hi Chris - sorry but I don't think Jodie's suggestion has been implemented.
From what she said, my own experience and David's second post you still can not reconcile a bank statement item against a payment on account, ie this is still a fault with the system.
To explain more fully. Someone pays you Â£100 on account so, using the system above, you enter it into the bank and against the customer's record via Money In in the Sales menu. You then upload the bank statement and try to explain the Â£100 but you can't. If it was paying off an invoice or matching any other manual receipt already entered (via the bank menu) the entry would appear on the list to "allocate" or "reconcile" but if you've entered it via the sales or purchases menus, it's invisible on the bank import screen.
This leads to the daft situation, as described by David, of having to delete the entry from the statement and, if you want to reconcile your bank account, having to go to the bank account, find the Â£100 you entered and "reconciling" it with a green tick.
So, to record a payment on account of either an invoice or bill, I'd avoid this feature altogether and just enter it via the bank in & out naming the customer or supplier to make sure it's recorded on their record, then when the final invoice/bill goes out or comes in, I'd enter it as usual but enter the initial dummy entry as a negative line in the invoice/bill (this also makes sure you are VAT compliant - see below).
You can enhance this process by putting the initial money in or out to a balance sheet account if there's going to be a delay in the final invoice or bill, especially if the delay spans a year end.
David (and Chris) the other main problem with this feature is that there's no VAT reporting, in that, generally, VAT has to be recorded at either the invoice date or the money date, whichever is earlier.
To be honest, I wouldn't pay anything on account without a bill and always send out an invoice with "Payment on Account" if I need clients to pay up front.