1) The best way to do it is to use the Exercise App, manually starting and stopping it from wrist, eliminating any question of whether or not it will get detected, and using the actual recorded data.
See How do I track my workouts with my Fitbit device?
2) If you will not use the Exercise App, you have 2 choices:
a) Just leave the data as is, which gives correct daily stats but doesn't let you see the stats breakdown by workout.
b) Manually log it after the fact, which is intended for cases where you were not wearing the tracker. In this case, it overwrites everything that was recorded, and gives calories, active minutes, etc based on the parameters you select when logging it. So no, it does not credit the workout twice, but it also is probably not quite accurate.
Incidentally any manually logged steps will not count in challenges, only data actually recorded.
Before posting, re-read to see if it would make sense to someone else not looking at your Fitbit or phone.
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