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.
Go to the Layer menu and select Pre-compose...
Make sure the Move Attributes to New Compostition is selected.
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.