I have taken several companies fully paperless on both customer and vendor processes. I'll explain lightly different approaches I have used.
First and most importantly, documents such as PDFs and spreadsheets can be stored via Document handling against any record in the system that makes sense. The most important aspect of a paperless system is attaching documents in a place where they can be found later intuitively. For example, should a signed sales order packing slip be attached to the sales order itself, or the customer packing slip journal that generated the source paper, or against the customer invoice journal that it ultimately posted?
Beyond that, the technical details behind attaching paper and non-paper documents via Document handling follow several paths.
You will have incoming paper. You cannot control what vendors are able or willing to send you. I have modified the Document handling form to use WIA (Windows Image Acquisition) to retrieve multiple scanned images from an attached document scanner, combine them into a single multi-page PDF, and attach them to the reference record. Then, from a pending vendor invoice or purchase order packing slip posting form, a user can click New -> Acquire from an open Document handling screen with paper ready in the scanner, and they are scanned and attached in short order.
Next, you will also have electronic documents, probably as attachments in e-mail. While it's not overly painful to save them to a temporary folder and then attach them via Document handling using New -> File, it goes a lot smoother if you implement a drag'n'drop target on the Document handling form. Then when the user drags an e-mail, say a customer purchase order, from Outlook to Document handling, the text of the e-mail and all attachments are automatically added to the order itself. From there you can arrange all inbound faxes to arrive as PDF files in the Inbox folders of your users, who then enter directly from Outlook into AX using a dual-monitor setup, and polished with a drag'n'drop of the originating e-mail.
Finally, you will have outgoing paper as well. Your drivers may need to hand over paper packing slips to customers, and collect proof of delivery signatures, which you'll want to keep. For this, a barcode can easily be added to the packing slip report. Once a batch of signed packing slips arrive back at the office, they can be scanned on a scanner with a document feeder like a standalone multi-function copier and delivered by e-mail to a user. Then AX with some programming can split that multi-page PDF into many single page PDF's, and then with the help of 3rd party software read the barcode off each document and attach automatically, leaving only the handful of documents for manual attachment that could be not read, i.e. barcode is torn or written over, etc. I have seen hundreds of barcoded documents attached automatically in a couple of minutes this way.
Of course, these days you can probably avoid printing any invoices at all by delivering them all via e-mail or fax, but there's no need to store or attach anything into AX from that effort since the customer invoice journal will remain around forever as a reference.
Hope this gives you some ideas.