Best Practices for PO to Payables Invoice Matching with Variance?

I am new to implementing and using the Purchasing module, and I have a question about PO to Invoice matching.

For example, if a single PO for $500 is issued and matched to a single Payables invoice in the amount of $549, how should the accounting distributions be handled for the Payables invoice?

In testing this scenario, I can match the invoice to the purchase order; however, I am unable to validate the invoice using invoice validation due to the variance between the invoice amount versus the invoice distribution amount.

Thanks