I don't know the answer (I use ProSeries, not Proconnect Online), but have you tried typing in a large number and checking what shows up on Schedule C?

For example, if you enter $10,000, does Schedule C show $10,000 or does it show $5000 plus some amortization?

Thanks for this. I can see how to input it now. 

You should run it  through the depreciation area, under amortization under code section 195 which says start up costs or just use the override on the schedule C input that you showed in your question.