Enter the two W2s as if they were one. I misread your original question a bit. You are filing as a Part-Year resident in California for the portion of time that you lived there. That amount is reflected by the fact that the CA amount is lower. On the W2 screen, enter in the Federal and Illinois amounts, and then you'll see an option to "Add another line". Click on that, another state line is made available, and then you can enter the CA information.
The rest of my answer is still true: CA and IL tax the same income, but only the portion that you made living in CA is taxed in both. With this modification, you may see your tax decrease (or your refund increase) for CA.
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