Hi - I'll have a guess at what's happening.
Your supplier has sent you bills and credit notes and both have been recorded on the system? If so you first have to set off the credit notes against the bills, to do this view the bill and then, at the bottom of the screen you'll see the credit notes and this will enable you to offset some or all of them against each bill.
You will then have bills, net of credit notes to pay off but you don't do this via Purchases > money out (see below) you do it via the main money bank section when you explain or enter bank entries into each bank account.
Finally, if you do ever do get to the point where a supplier sends you a credit note and a payment (because all bills have been paid off) then you don't enter the cerdit note, you enter the bank receipt into the bank account using the Refund tab.
Both sales > money in & Purchases > money out are for payments on account, ie if you receive or pay money on account of an invoice or bill that will be raised later on. I generally advise people to steer clear of these sections unless they are certain each payment will match a later invoice/bill AND if they are not VAT registered.
Hope that's of some help.