When filing out the 1099-misc it asks "Was any part of the lawsuit settlement for back wages?". Would the 1099-misc income ( which is on box 3 of the form) have back wages included in it or would only the W-2 have that?
The 1099-MISC should only report the settlement portion of the payout. The W-2 should report the wages (back or otherwise) and appropriate tax withholdings taken. You will need to review your settlement agreement to ensure the forms are reported correctly. If you find the 1099-MISC reports more than it should, you need to contact the issuer (payer) and request a corrected form.
In general, the part of the settlement that is for back wages should be reported on a W-2 and is subject to social security and medicare tax. Any portion of the settlement that is for punitive damages, interest, or other non-wage damages should be reported on a 1099-MISC, and is taxable income but is not subject to social security and medicare tax.
The question exists because some payers send the wrong paperwork. If you don't know if there are wages in the 1099, you need to ask the settlement attorney. But it sounds like you got the right paperwork and there are probably no wages in the 1099 amount, just the W-2 amount.