Node newbie question (content/partials/layouts)?

Still a newbie with Node/Content/Partial/Layouts and have some questions…

Where do I include items such as the local storage manager? Currently I have them in the layout page but when I try to clear the cache for example it fails, so included in the content page which works fine… And how about other features such as Lightbox, Data Store, infact all extensions?

What is the best practice here, as for the life of me can’t find any information on the Community? Is a subject also lacking from the documentation as far as I can see…?

Any advice from the experts appreciated!