Investors & landlords

My 1099-Misc has amounts in BOX 2 (ROYALTIES) and BOX 3 (OTHER INCOME).  I input both amounts for that 1099-MISC. as prompted by the software.  When I create the “OTHER INCOME” amount into a SCH C for the oil and gas drilling business it does not remove it from the 1099-MISC entries, thus showing the amount twice.  Some TURBOTAX responses reply that an option is NOT to en enter the BOX 3 amount for that 1099-MISC if creating a SCH C for that entry.  How should I handle the BOX 3 issue?