Sounds like he wants to do retroactive withholdings of your portion of fica/ss which is fine. The risk here is that he sends so much of your paycheck(s) to the IRS that you have short term cash flow issues.

I agree if you got a 1099 for 2017 and already paid the IRS this should only be for 2018.

Is he having you do a w-4 and going to start withholding for income taxes too? This could all end up being more than one paycheck.

Have you been making estimated tax payments?

Btw he may try to make it that you need to pay the 7.5% he is going to have to pay now that you were actually an employee. I don't think tht would be legal so watch out for it.