My preference is to take the limit from the smallest prize that covers the limit and then put the remainder in the next prize such as below (equivalent to taking it from the specific place and rolling the remainder to the next prizes):
12,0000-6,000-limit2,000-2,500-1,000-800-600-500-400-400
Others can do it differently, including not distributing it. In the National Open and CCA events I’ve worked it has been distributed.
Some pairing program distributions do the limit and only indicate that the amount needs to be distributed rather than doing a distribution. If the TD and organizer overlook that then it isn’t distributed.