In order to enter a 1099 from you as an individual to your company you'll need to do that separate from your tax return. TurboTax has a center set up to do that and you can find it here.
However, the only reason that I would recommend that would be if your client issued a 1099 to you as an individual for the money that they paid. If they did that - if your social security number is on the 1099 that they sent you instead of the EIN of the company - then the 1099 is necessary in order to get the income away from you and on to the company's tax return. In that case you would need to create a schedule C business on your personal return for the income and show a matching expense for the transfer.
If they did not issue you a 1099 with your social security number on it then you have an awkward accounting situation where you were paid into one bank account and moved it into another but a 1099 isn't necessary to deal with that. It just means saving your personal bank statements along with the company's in case you are audited. But it will show a deposit and a matching transfer every time so it should just be entered as income into the company. A 1099 is a waste of time.
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