The AttachmentSvc has all of the DocStar Methods. You can make a folder and upload, but you would lose all of the builtin functions.
You can make each customer a Document Type which will make a folder, but then you have a ton of folders showing on every customer.
I am not sure what the purpose of this structure is. ECM is going to search by Keywords and CustID is set by default, so even in a single customer folder you can get one customer in a search and they only show on the customer record they are attached to in Epicor.