Separate directories for dynamic and static files

The web server I am using requires me to put all the dynamic code in one directory and all the static code and images in another so I was wondering what would be the easiest way to accomplish this. What are the easiest ways to accomplish this?

I am a web programming newbie, but have some experience programming other languages, so I was thinking of writing a script to change some URLs in the Gallery code. However, I am concerned about whether doing this will make it difficult to upgrade Gallery in the future.

Thanks in advance.