Yes, if you are filing a tax return for him, all income from all sources included all W-2's need to be included on one return.
No, there is not an exemption for work study. it is likely that the amount he was making was under the threshold for having taxes withheld. If he was paid less than $14,600 in the year he would not need to file a return, so if his weekly pay would come out to less than that, then they would not have withheld taxes unless when he filled out his W-4 he would have indicated that they should withhold more.
If not having taxes withheld causes him to owe, you will just need to make the payment when filing the return or set up a payment plan or you can choose to file now and then pay later. TurboTax will give you all the options for paying a tax due.
For the city, if they did not take out taxes, you would still file it normal, including all income on one return, and then you may have to send a check in with his return to pay what was not paid if he has an amount due.
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