In terms of organizing them in the explorer, that is really up to you. You should set a folder in settings for where you would like attachments to be stored by default. If you don’t do this they will go directly into the vault root when you, for example, drag and drop an image into a note.
If you look around the forum, you will see it is very common to create a table of contents for related things, often referred to as an MOC (map of content). There are plenty of posts explaining that process, and it is definitely a good habit to get into as it is more flexible than relying on organization in the explorer.
Embedding files is a good practice to quickly compile updated content from notes or files with just a link to the file with an exclamation point before it.
I hope this helps point you in the right direction. This forum is a great place so you will be just fine, I’m sure.
