I paid a supplier twice in error. I don't want to allocate the second payment to another invoice. How can I allocate this to the supplier but not to an invoice?

Hello Joss at Zoomadog, thanks for posting on the Community page, so you can a supplier refund instead if you do not wish to do a supplier credit. If you have a look at this article it tells you the steps you need to do to record this in your account. 

Hi @Joss at Zoomadog 

Two options:

(1) Enter a Bill Payment (against an unpaid Bill from the same Supplier) but then untick the box against the Bill.  Enter the actual (over)payment amount on the Bill Payment - this will go against the supplier account as a credit.

(2) Enter a Cheque to the Supplier with Category set as Accounts Payable with NoVAT code.  This will enter a credit against the Supplier ledger that can be used at a later date (it will show as a credit in Pay Bills).

Hope this helps.