Just enter the information as it appears on your W-2. You will have two lines of state information (boxes 15 - 17), one for NY and one for CT.
If you got two separate W-2s, one for each state, enter them as if they were one W-2 with two lines of state information. See the following FAQ.
How do I handle multiple W-2s from the same employer?
When you finish your CT tax return, before you file it, check to make sure that it shows the correct total wages, and not double what you actually earned.
