To move a document into a different folder:

Click the Documents tab.
In the Documents table, click the name of the document you wish to assign to a folder. The document image will now display on its own page, along with a Summary box.
In the Summary box, click Edit. This displays the Edit box.
In the Edit box, in the Folder field, click the down arrow to assign this document to the folder you desire.
Click Save. This displays the Document Processing page, which indicates you've finished processing this document.
Click the Documents tab. The document you just assigned to the new folder now displays in the Documents box.

In order to associate a document from one folder to another you must select the document you want to change and click "edit." From there select "Folder," there should be a drop down box with a list of possible folders to move the documents to. For more information regarding assigning documents please refer to the following link:
https://app.bill.com/help/Assigning_Documents_to_a_Folder.htm