The Convenience of the Employer rule does not apply to you since you work in MA. Connecticut only applies this rule to nonresident employees in Arkansas, Delaware, Nebraska, New York, and Pennsylvania.
So you are correct. Since you are a resident of MA, you will fill out your CT return first and get a full refund as you have $0 income taxable to CT. You will then need to pay MA taxes on your full wages as a resident of MA.
You should also change with your employer, the state they withhold taxes for so you can avoid this situation next year and avoid any underpayment penalties for not having any taxes withheld in MA.
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