Right now it will be only added to the memory for the current project.
When you add it to the library using the component it will be in the memory and won’t be written to any file (I know what you are thinking about now, read the next one).
3 & 4. In case you have materials and constructions already created just copy them to “LadybugFolderOnYourMachine\userCustomLibrary.idf” and it will be loaded every time you let the Honeybee fly. This is your custom library and won’t be ever overwritten. You can copy any standard material, construction or schedule and it will be added to Honeybee library.
These are all very good questions that should also have answers in the video tutorial series. I think I will put up another video at some point that shows the workflow for adding constructions to the userCustomLibrary. When it is up, I will post in here so that other users that find this page will know.