To change the folder a document (or file) is stored in, first edit the document (file) by clicking on the blue Edit command next to its name. Then select the new folder from the folder drop down list:

Once you've selected the new folder, be sure to click on one of the save commands.

If you want to move all the documents from one folder into another (and have the first folder deleted once it's been emptied), use the Combine Folder command. Click on the 'Customize' command on the blue bar, then choose the Modify folder settings command at the bottom of the screen, choose the folder you want to combine from (empty out) and continue following the screen prompts.

(move file, move folder, change file folder, change folder, move document, change document folder)