Yes, you have very good hearing .
You should have in company folder per-company sub-folders named after company prefix: 0, 1 etc. In every company sub-folder you should have at least following directories: js_cache, backup, images, pdf_files and reporting. Normally all this per-company tree is created when you start new company. These are working directories for various FA modules made to separate company of each other.
Simply try to add new company and you should end with described directory structure.
PS. The directory structure is the same on Linux as well as Win. I also use Linux, so you can trust me .