"_If_ tax is due on the NR portion it will have to be added because the software will not include it automatically."

Where should the tax due on the NR portion be added on the 1040 form? Which schedule/line?

In this case, the cx started as NRA, but ended the year as RA.  So, the 1040 is the dual-status RETURN and the 1040-NR is the dual-status STATEMENT.