Most of the effects have the option to change settings at keyframe level.
Drag the required effect to the fx line in the timeline. Select it and click on modify. Depeding on the nature of the effect a number of settings can be changed.
If you click on the keyframe button at the bottom also at keyframe level. Some effects have the option to change a mix % with the original (example look at Emboss).
In case they don't have that the trick is to duplicate the "effected" videopart and put that in parallel with the original on the separate track. The effect video above the original. Then change the opacity from 0% (not visible) to 100% completely visible. Which has the "effect" I think you are asking for: the effected part is fased out.
There are some excellent youtube tutorials that explain all this:
https://www.youtube.com/watch?v=V8cosdWggDw
Have fun.
Warry