How to structure a wordpress site in folders?

I would suggest a combination of using pages for the parent directory content and comments handling e.g with the slug/cars-home/ and a custom post type to gather each single cars e.g. /cars/red/.

-- /cars/red/ (single CPT)
-- /cars/blue/ (single CPT)
-- /cars/white/ (single CPT)

--/cars-home/ (page)

Next you can either add a custom loop to include a loop querying the car Custom Post Type, or you can call the cars-home page inside your car CPT archive template.