I do this on almost all my templates. I don't think the “highlighted layer” idea can be done in the way you're thinking, but you can absolutely create a control layer in the main comp that sets parameters in other comps. That's what expression controls are for.
Create a null or adjustment layer in the main comp and name it “Controls”. Go to Effect > Expression Controls > Color Control. You'll need one control for each element you want to be customizable and name the controls accordingly. In the Effect Controls window, lock the view of those effects, then navigate to the precomp. Any color effects with a color picker like Fill or Tint will easily work with a color control. Expand the effects on the customizable layers, alt+click the stopwatch next to the effect's color property and then pick whip the corresponding color control's color property. This will link the properties together and the color will be editable from the main comp, without the need for a user to randomly search through precomps and layers, or have any sort of advance knowledge of AE. I hope this was helpful. Good luck.