Some effects actually come with opacity attributes that can be animated/keyframed.
For those effects that don't provide that option, or if you want to pursue a different path:
- Duplicate your effected layer
- Remove all effects from the bottom of the two layers
- Animate the Opacity of the top layer from 100 to 0 over time
You can trim your layers in the timeline to only take up the time spans needed.
Depending on your timeline layering, you could also consider using Adjustment Layers, or possibly precomposing to acheive your goal.
for those effects that have the opacity attributes, is it acceptible to just change those (opacity) settings the other way alone or should I look out for other setting too?
If the effect has it's own opacity settings (i.e. - Trapcode Shine), you can fade out that effect simply by animating that attribute.
Many (most) effects do not offer that option.
It may just be easier to duplicate your layer as mentioned earlier, and animate the layer's Opacity.
The layer's opacity is always an option. it exists regardless of the presence of an effect, and as such, may be a more reliable solution for you.