I found the manual entry to be lackluster. You can label an activity and enter the amount of calories burned but regarding active time, it defaults to however many "steps" the sensor picked up during the exercise period. This is fine for running, walking, aerobics and the like but not so much for weight/circuit training, elliptical training, and especially cycling. That is why I prefer the link with Endomondo. Based on the type of exercise you are doing (especially if you are using a HR monitor), it "knows" whether you were working hard throughout and will override the step data to credit you with more "very active" time. It will not generate added steps but it will generate the active minutes that fitbit needs to present a more accurate measure of your activity level. For what it's worth, if you prefer something like Runkeeper, you can import workout files to Endomondo and just use it as the middleman to get your activity uploaded to fitbit. I prefer using the Motoactv for my outdoor runs, so I do this regularly. It must be .gpx, .tcx or .fit and be no larger than 10mb, but that allows some flexibility to use other programs.
