For Timed workouts, generally a time cap is programmed for the purpose of keeping the day on schedule.
There are a couple ways you can rank athletes that do not finish within the allotted time, depends on how you program your workouts, here are your options:
Option A: The easiest approach is turn on the time cap option in the workout editor. This will enable a new option in the score entry page called TC, simply click TC, and enter the completed reps. (This is a natural transcription from the scorecard to the system)
Note: If you bake in a tiebreaker of any kind, you will need to go with Option B
Option B: You can add 1 second for every repetition not completed (this is not always directly obvious on the leaderboard and requires a bit of math (which lends possible entry errors), check out WOD 2 of this example, which has a 16 minute time cap).