Well I think the phrase 'wordpress doesn't use folders' is wrong.
I've also been finding it hard to do this exactly, I have found plugin's that enable users registered with your wordpress site to have access to an FTP access tool (the plugin appears under the tools section) which lets them download and upload files. (ACCESS TO FOLDERS!!) I'm using this with another plugin called User Access Rights, where I have created new user types (like subscriber/editor) I have made one called clients, they have absolutely no rights, apart from the access this FTP tool, they login through WordPress, get to the dashboard and can access the FTP plugin only to upload and download.
However my problem is that I can use the actual FTP Usernames & Passwords to set restriction to specific folders, my clients can go all the back to the root, which is a no no. Also id much prefer to have the FTP files appear on the Front end of the website, and not have to login to the Admin/Dashboard to access these files. So that the header and Footer are there for branding, I don't want my clients to know what CMS I am using.
Graccuris, did you have any luck?