You've asked quite a few questions in one post. The following answers are pretty general. Specifics can vary depending on the operating system you use and the file types specified for your media.
References to media may be stored in fields of type container. Physical copies of image files, but not video clips may also be stored in a container field.
Since you have many such files to associate with a given record, you should use a related table of records with one container field in each related record. This allows you to link any number of media file references to the same record. You could define multiple container fields in the same record, but then you are limited by the number of container fields you define where a related table has no such limit.
How would you script setting up folders, if they don't exist, which the media is stored in (naming folders, how many)? Do I need just two folders named video and photos to store all media?
I'm not sure what you have in mind here. Your stored references will not be organized in folders, they'll be organized in records linked via relationships to the specified record in your main table. If you mean folders or directories on a computer hard drive, you can organize them into as many folders as you wish, but a FileMaker script cannot create or modify folders. A FileMaker Pro plug in or a system script such as Apple Script would be needed to automate creating folders on your hard drive.
From a user perspective, how would you script importing media to those folders?
You would create a script to automate the process. Such scripts can import all media file in one go with the Import Records | Folder tool or you can create a script that allows you to select and import one specific file at a time. A FileMaker script can be created to move image files from one location to another as well.
How does filemaker reference media files stored in a folder?
Unless the file was an image file and inserted as a physical copy of the file, the container field stores the file path to the file and uses this file path to access the file in order to open it or make a copy of it.
I'm importing a an image file as a reference linked to a particular record. That image file just happens to be on my desktop. Or I'm importing an image file from a camera linked to a particular record. How would I/FMP store the original image file? Do I need manually set up folders to store the original image file. Can I script the folder setup? If I store a reference and then delete the original file I've lost the image. Maybe I'm missing something really simple here...
As I have already posted, FileMaker cannot create new folders on your computer. If you have the skills, you can create a system script that FileMaker performs to create folders. There are also third party Filemaker plug ins that can create new folders for you.
What FileMaker can do is use Insert picture to insert a copy of or reference to the file into a container field and then use Export Field Contents to create a new copy of the file at a location specified by you or the script. It cannot create that location for your without outside help. (But in windows dialogs, at least, you can manually create the new window as part of the export field contents process. I would guess that you can do the same in mac systems but can't confirm that guess from here.)