Are you sure that it isn't just a matter of the button having been removed from the toolbar? Can you confirm that the clipper is truly not installed by going to Safari>Preferences>Extensions and seeing whether the Clipper is in the list of installed extensions?
If does appear in that list, return to your browser window right/ctrl-click on the toolbar and select "customize toolbar" and drag the clipper icon to the location of your choice on the toolbar.
So: Stacks contain ONLY notebooks Notebooks contain ONLY notes
So you can have a stack called "Business" filled with several notebooks: Perhaps "Articles" and "Products" In "Articles" you create notes that contain.... articles or whatever. "Products" you put notes that relate to product info.
Now, this means you can limit a search to your business stack, for example: stack:business gruntmaster2000will search for both articles and product info for information on the gruntmaster2000
Perhaps you want ONLY product info on the gruntmaster2000 so you would search notebook:"products" gruntmaster2000This will ONLY bring up product info and NOT articles.
You can use tags too. Lets say one note for the gruntmaster2000 product isn't really working for you. You can have many gruntmaster notes, and tag them all with gruntmaster2000.
There's LOTS of discussion throughout this community about how to organize. Some links to get you started: https://discussion.evernote.com/topic/21329-effective-use-of-tags/
This one for sure: https://discussion.evernote.com/topic/33175-organizational-structure-in-the-stacknotebooktag-ecosystem/