My company A performance services for another company B. We had a legal contract signed up before the work. All my invoices were sent from Company A requesting check to be made payble to A. However, the Company B sent checks in my personal name and then after the end of the year also sent a 1099 in my personal name. In the mean time, I have paid my employees using that income and sent their W-2's and paid their taxes. What are my options now? Do I have to show a big loss for the corporation (since it doesn't really have the income) it was supposed to have. Do I have to show a big income on my personal schedule C? Or can I simply put a not in my taxes that the 1099 was really not for me but for my corporation? The big loss will take years to recoup on my personal income taxes at $3000 per year. Please advise.
No one at the big company B is answering my phone calls to allow correcting their mistake.
Thanks.

You will need to report income on schedule C (Form 1040). If you paid the amount received by you to company A, you can claim that as your expenses so net income is nil.
If you did not pay it to company A, report your expenses (how you used that income).

Thanks MukatA. That's helpful.