How can I make some sub directories so that all the other info is not in the same folder as the published exe?

Sadly, I don't think this is possible with the A5 engine. I hope that Conitec implement the feature in the future.

The Fang.

Make your subdirectories and then add the proper path statement.

For instance I have the following subdirectories under my game

Models
Images
Sounds

In my wdl file I have the following

path "Images";
path "Models";
path "sounds";
path "C:\\Program Files\\GStudio\\template";