This deserves a bump, as nobody ever answered and I think there are some good questions here.
These questions would best be answered by your VAR during a detailed demo of EPDM. I will try to answer for other's benifit, but answeringt these questions will bring up many more.
The best way to keep files together is to have a Change Notice/ Work Order document in EPDM and attach your files to this docment. I did a presentation at SolidWorks World 2011 on automating ECx process. My presentation is on the downloads page my web site www.wlmservices.net.
You really do not assign work in EPDM. The notifications are a way of letting someone know that work needs to be done.
cc copies would have to be done via a custom program if you want to send someone an email that they need to do work and copy others to let them know someone else is doing the work.
Automatic alerts and due dates would also have to be a custom program. Now you can generate reports on the length of time a files has been in a state. I have a task addin on my website that does this.
If you select a single file and change it's state, only the appropriate transition names will be available. Unfortunately if you select a folder and change state, all transitions will be listed since the files could be in different states and or workflows.
You can send dynamic notifications where you pick a user for a list of users and only that user would get the notification. This would not prevent someone else that has permissions to do the work though.