You can optionally mark a stage as "Limited" or as "No FTN."
What's the difference? At 2012 Nationals, there was one stage that wasn't shots-limited but had only disappearing targets. Hence, no FTN on the stage.
Marking either of these options for a stage will keep you from inadvertently entering an FTN into the score.
Also, if you're using the "narrow" score sheets, the stages that are not eligible for FTN will be printed accordingly.