Here is how I use layers as input source without affecting my composition:
1) I create a mask layer where all the clips are a "FFGL Source - Solid Color" with compositing mode to "Add", Opacity (V Slider) at 100% and Brightness parameter at 0% to create a black slide
2) All the layers I'll want to use as input source, I place below my mask layer so that they don't show in the overall composition.
3) If you want to use any of the input source layers in your composition, you can use the Sources:Routing:Layer Router in a different layer.
If you don't use the crossfader A/B, another quick way to do it is to put set the cross fader to A for your composition, and change all the input layers to bus B. Note that you don't even need to change the composition layers to bus A for this to work.
Let me know if any of this is not clear.