How to install python scripts or addons

When you open the addon panel under preferences, and you see the list of addons, do you simply have to put a check mark in the box on the right side of the addon, and it will be enabled, or do you have to then click install from file at the bottom left of the page, go to your addon in your addons folder, click on it and then click on install from file at the top right of the page. What about the ones that don’t show up in the panel. Does it hurt to install files more than once. I have not yet made a separate folder for addons I have added to blender. They are all in the addons folder with the scripts that came with blender. Because it takes time to figure out which are installed and which are not, can I simply install everyone, as I have outlined above? What about the scripts in folders with multiple files? Do you just click on the init file and click on install from file or do you have to click on each of the .py separately and then click on install from file? What if you have multiple folders within folders, and these multiple folders all have .py files within them? In what order to you install the .py files? As well, aside from theme files that get put in the presets folder, are there other types of files that go elsewhere. What about blend files? How do they work? What if you get a blend file and a .py file in the same folder? When you have a zip folder, no matter what kind of zip,(rar or otherwise), do you simply click on the zip folder and then click on install from file? If I want to install the hoverbox xml file, do I simply put it in the presets folder. Can I use the file that is already in the scripts folder or do I have to use the file with the same name that I downloaded with the hoverbox file? As far as errors go, that I see in the console, is there a resource available that will help me interpret these errors and enable me to install the .py scripts? Thanks.

I have read what the manual has said about installing scripts. Is the addons_extern folder mandatory or will the added addons work out of the addons folder? Is the addons_contri _bundle folder a separate folder. Should a blender user have these 3 folders in the scripts folder? Can a person have to many .py files in the scripts folder? What does it mean when the scrolling of the addons panel reacts very slowly? Will duplicate file names mess things up? Thanks