Hi vlturno:

To enter this in Simply Accounting go to your purchase invoice screen, select the bank the cheque is to be deposited in, put in the cheque number or reference number from CRA for the invoice number, enter the date and code the overpayments in the associated expense accounts (CPP expense, etc.) as negatives. Income tax overpayment could be posted to a miscellaneous revenue. The total should be the amount of the cheque. Check the report before posting the transaction/entry.

Hope this helps!