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Your income doesn't need to "match" the 1099. You are supposed to track Everything that is income, even if no one ever needs to report that to you and the IRS on a 1099-Misc form.
Your income is Gross. The amounts held back from you are your expense. That's what others should be reporting to you. Example:
Your Gross for a sale is $15,000 but the Check to you is lower, because someone held out your share of some commission to another and your share of Advertising expense.
Your Income still is $15,000. Your Banking is lower because there are costs heldback. You need to enter all of it. You might even need to send a 1099-Misc to that other party.
Ask your CPA to help you know what is what.