How to orginize template folders?

Are you referring to the folder structure within After Effects? Or the folder structure of your actual ZIP ?

Either way, there’s no specific structure we require. We only ask that both aspects of the project remain as organized as possible. Grouping similar types of items into folders with logical folder names. Like placing all of your audio into a folder titled “Audio”. You could also add sub-folders for things like “Effects” and “Music”, if you were including these things.

When dealing with the organization of your ZIP , it’s always preferred that you provide only your Project File and the Help file in your root directory. Then add an assets or footage folder in the root as well, and place any included assets into that folder. Remember to do this before saving your project the last time, so everything links up properly once it’s extracted by the buyer.