Pre-Comps

When you have too many layers in your timeline it is a good idea to create Pre-Comps.

The first thing you do is select the layers you want in the new Composition.

PreComp Layers

Go to the Layer menu and select Pre-compose...

Precomp menu

Make sure the Move Attributes to New Compostition is selected.

PreComp window

Notice that you end up with a new Comp icon in the Project Window and Timeline.
Doubleclick either of those icons to open that Comp and adjust the layers inside of it.

PreComp in Project Precomp in timeline