ProSeries does not limit due to Basis.  You need to manually do that by only entering the allowable amount (if any) on the K-1 worksheet.

You will also need to manually keep track of unused losses for future years.  When allowed, you will need to enter those unused losses by entering a separate K-1 and name business of that K-1 "PYA".  You may also need to check a box about using that on page 2 of Schedule E.