As suggested by Erika, you need to learn about "Views" - each of which has an associated layer combination. Typically, once views are set up, you work almost exclusively in views.
If you need a 3D view with all layers on, create such a layer combination, and create such a view.
Do note that there is only one active layer combination for all modeling viewpoints - plans, sections/elevations, 3D, etc. So, if you switch viewpoints in Navigator you will not change the layer combo. If you switch VIEWS, you will also switch to the layer combo saved with the view.
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