Here are some best practices when organizing your theme folder to make things easier to find.
Keep these files in separate folders like so:
theme-name/js/ theme-name/css/ theme-name/images/
or you may want to organize them into an assets folder like this:
theme-name/assets/js/ theme-name/assets/css/ theme-name/assets/images/
Put all your template files into a templates directory, then further separate them by the base template type (ie. page, node, block, view).