A clean project structure becomes extremely important once your composition starts growing.
Instead of keeping every asset in the root of the Project panel, create folders such as:
Compositions, Footage, Images, Audio, Precomps and Exports.
Naming is equally important. Names like Shape Layer 47 or Comp 12 quickly become confusing. Use descriptive names such as Logo Animation, Main Title or Background Elements.
The same rule applies to compositions. Separate complicated scenes into precompositions instead of placing hundreds of layers inside one timeline.
Color labels can also help distinguish different types of layers.
Organization might feel unnecessary when a project contains only ten layers, but it becomes extremely valuable when you return to the project weeks later or need to send the file to another editor.