One of my favorite things about managing Web Orders, Estimates, Files, and Proofs is the Online Print Center “Dashboard” from WebsitesForPrinters.com. See the snapshot below for all of the detail. The blue numbers are the actual number of files that you can click on and get a detailed list.

Our customers can upload a file and it gets assigned a number, say #1234.
We then attach a proof file to that same #1234.
Then they respond and their response is still attached to the same #1234.

At any time this file can be converted to an order. In fact, it can start at the estimate process. The beauty is that the entire order and all of the files, proofs, responses, plus files added later (by us or the customer) all stay together. On top of that, the customer also has access to the files at any time too.

And, to help with communication, there is a job journal attached to the order that allows you to record communications.