Unfortunately, Proseries is severely deficient in this regard.  There is no place to enter the Basis to have the program limit the losses.  You need to limit the losses manually. 

When entering the K-1, only enter the allowable amount of the loss (if any).  For the carryover, make note to yourself so you can manually enter the carryover next year (enter the allowed carryover amount as a separate K-1, called "PYA").