Bill.com provides the option to associate a document with an existing bill

Steps

Once a bill has been sent to the Inbox:

1. Click the Inbox tab
2. Locate the document
3. Under Add to Existing, click Bill
4. Select the Vendor
5. Click Search
6. Select the appropriate bill the document applies to
7. Click Save

You will see a list of the five most recently processed items in the "Process item by:" window - this will allow you to add a new document from your Inbox to an item you have recently processed.