Masters can be organized into folders and reordered in the Masters pane using the toolbar and context menu as well as drag and drop functionality.
Click the arrow buttons in the Masters toolbar to move masters and folders Up, Down, Indent, and Outdent.
Right click a master or folder to open the context menu.
The Move menu in the context menu allows you to move the master or folder Up, Down, Indent, and Outdent.
Drag and Drop
Click and drag a master or folder and drop it on a folder with move it to the folder. Dropping it on a master will make it a sibling of the master.
A Folder can be created by clicking the Add Folder button in the toolbar or right-clicking as selecting Add->Folder.