First, if you haven't already, you should enter as one W2 with a line for each state for boxes 15-17. You are correct the box 16 amounts for each state will be different as PA taxes the box 12 retirement contributions and DE does not.
After verifying these entries you would answer "Yes" the DE wage income is taxable by PA. There is double taxation and you will claim a credit on your DE resident return for taxes paid to another state (PA) on the same income. You will do this in the credits section of your DE state interview.
I recommend you complete the PA non-resident return first and take note of the tax paid to PA on the wage income. You will use that number to claim the credit on your DE return.
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