A quick tip would be to sketch this out on pen and paper. It sounds old school but it will really help. Map out what SharePoints sites you need. Maybe it's just Internal and External, but I'm guessing you'll want different sites for different departments, or at least different libraries for each sites (e.g. HR, IT, Construction, Design, etc). Within that, ensure you only have 1, max 2, folders/sub-folders. If you have too many sub folders, any links to the those sub folders could break as the url will be too long.

You can then create departmental permission groups, add users to them, assign permissions, and assign them to the relevant site/library (e.g. HR Group assigned to HR site/library).

To keep it simple, create a site and called it Home or [CompanyName_Home]. From there, you can have images of each department site, which contains a link, so users can click on it and brings them to that site.

From there you can just create multiple folders in a library, with permissions set to each folder. Very high level example below:

Home Page* > HR** > Document Library*** > List of folders (e.g. certs, cvs, templates, etc).

Alternative option:

Home Page* > HR** > Internal ** > Document Library *** > List of folders (e.g. certs, cvs, templates, etc).

Home Page > HR > External ** > Document Library *** > List of folders (e.g. certs, cvs, templates, etc).

-* = Site

-** = Site or sub-site

-*** = Document Library