Use the FileFolderService.move(sourceNode, targetParent, targetfilename) method. First find get the NodeRefs of the document you wish to move and the folder you wish to move it to (you can use FileFolderService.resolveNamePath(root, path) to resolve a path String into the nodeRef that that path represents, just use String.split("/") to change your path into a List of path elements and work from a common root node like the Company Home)
Regards
Steven