My spouse owes an amount, but I have a credit. Do we have to pay his full amount and then I get money refunded to me? Or do we just pay the difference?

Yes, unfortunately one spouse's refund cannot pay for the other's balance due. You can however Netfile the one with the refund and wait till the last day of the month to Netfile the one owing. This would give a chance to perhaps receive the refund in the bank account by the time the other balance is due.

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