RIght - I was wondering if I needed to deduct the $10,000 to arrive at $45,000 ($55,000 - $10,000). The software does not transfer the $10,000 to the QBI worksheet on the S Corp K-1 worksheet. It would have to be entered manually (which is my question). 

Right - this is the issue you're thinking about regarding the IRS saying it's a double deduction.