I think we are confusing the OP.
In summary, you only want to claim your income ONE time, whether it be 1099, lumped income, etc. So, just follow your tax program. When it asks you to report 1099 income, do so. Then it will likely ask for NON 1099 income, so subtract it out, and report that.
Not too tough. If you get your taxes prepared, then your tax rep should know how to handle this.
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