I am making both a projector and a website in Flash MX 2004, using external
..as files in various locations.

Do I need to include the .as files with the projector and upload them to the
server alongside the .swf files? Do they work in the same way as external
Javascript & CSS files or are the scripts included in the swf/exe upon
publishing?

Many thanks

".as" files are compiled into your movie at publish time and the compiled code is included in the swf or projector. You do *not* have to include them with your projector or upload them to your server.