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I am assuming you are running Pastel Partner/Express - the steps in Evolution are different.
First check if you have both +ve and -ve amounts to the same supplier. Go to Process, Match Open Items, Select the supplier and the period you want to match the items in. Click the plus next to the unallocated amount. You can then click eg +2c and select and invoice to add it to by clicking on the invoice number. You can then match a -2c against the same invoice to clear it. Clear all your unallocated amounts and save the entries.
Then go to Process journals, select Supplier journal and input the date, period and amount (DR or CR). Either create a rounding GL account, or use discount received as the contra account. If you are not asked to match the transactions on completing the line, once you post the batch, go back to match open item and allocate the remaining cents against the outstanding invoices.
If you have suppliers where you constantly have rounding issues, change their input method to inclusive of VAT - then your invoice totals will balance. You can also use a GL code on their invoice, eg discount/rounding and put in a -2c at time of input.
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