Count the days for the last 5 years ... did the taxpayer use it as their Principal Residence for 2 years (730 days)?

If so, the way ProSeries wants you to do it is to 'link' the Asset Entry Worksheet to the Home Sale Worksheet, and report the sale using the Home Sale worksheet. 

ProSeries will incorrectly put the sale on 8949/Schedule D rather than 4797, but the end tax result should be the same.  If you want it to properly show up on the 4797, you could probably enter the exclusion in the worksheet on the top of the 4797 (enter it as sale of property, showing a loss of the exclusion amount).