Philippe,
I see. Well, there's no "accounts" per se with file uploads - it's just regular browser uploads to a website. What I'm thinking you mean is that you have separate companies and each have their individual, probably repeating or redundant, publication types and documents. What you'd like to do is create publication types that would be global to all companies or more than one company, am I right? If so, that's not currently possible, but I'm thinking it would be a valid feature request for a future release.
In the meantime, the only thing I could see that may help you would be to create a Public Company - one that acts like a regular website where anyone can create a login and place orders. Assuming you would do this, you could assign publication types and documents to that company only, and anyone with access to the PrintShop Mail Web interface could place orders for those documents, static PDF and file uploads.
This really depends on your business model and whether tracking orders for each company is important to you, and whether you want to restrict certain documents to certain companies.