I created a company with a business account, but for regulations with the client(NY Agency) the payments were being received in the personal account. Deposits were then being made from the personal account to the business account and I paid everything from the business account.
I have an accountant(only work the company not personal taxes) who does our accounting for the company, and he asked me to issue a 1099 for payments or deposits made to the business account.
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.