I received a 1099 with my ss#. The income was direct deposit to my llc bank account. The income was reported on llc 1065. How do I report this on my personal taxes?

I was instructed to put the income on schedule C and then put it in again as a negative number with a note “ paid to llc”.  The IRS reversed the negative and sent me notice I need to pay taxes the total ( which is 2 times the amount). How do I correct the Schedule C?