Thanks for the links. My T1 has already been adjusted by the CRA. I'm just wondering how to apply the T2125 to the balance that I now owe? Do I pay the balance first, or do I send in the T2125 first?

Normally the T1 adjustment would also be used to change the results caused by the input on the T2125.  In your case, I would copy all of the applicable receipts, keep the copies for your records and send the T2125 and receipts off to CRA with a letter asking them to reassess based on the documentation.