either automate the bypass on the effect using the automation lanes, or in the case of delay (for dubby effects, vocal delay), often its worthwhile to have a separate track with the delay FX on, and then automate a send to that track for the phrase you wish the delay to work on (kind of emulating what a live engineer would do). In a more general sense, split the item you wish to effect, right click, select item properties, and theres an FX button half way down the popup window. (or you select the item and click shift-e to open the fx browser.)