Quote: "When creating a game, do all of the files have to be in a specific location? For example, if I have a game I want to call "Hello World", do I have to have all the files (script, map, sounds, etc.) in a folder called Hello World? Do I need separate "Hello World" folders in each FPSC location (mapbank, scriptbank, etc.)?"
The short answer is
NO to needing the "Hello World" folder all over the place or in the different folders.
When you build a game, you specify the name of the EXE. When that is done (and if you use the "My Games" folder), you will notice a folder created with the name you specified and the "files" directory. The build will copy all the media and place in its proper folder structure you have already in that "files" folder.
Now, as far as your question, if you wish to have a folder in your scriptbank called ""Hello world" and all your scripts in there, that is fine. Same with custom huds, backgrounds. Your entities, segments, and textures for those do not need the "Hello World".
It is personal preference. For example in the Egyptian Development I am working on, all scripts go in a folder called "scriptbank\NFM\Ancient_Tombs1\". All our huds are in "languagebank\english\gamecore\NFM\Ancient_Tombs1\huds\" folder. All segments, entities, textures, weapons reside in their original location.

There's no problem that can't be solved without applying a little scripting.