Evernote, by design, sorts the Stacks and the Notebooks inside them in alphabetical order. There is currently no option to change that.
However sometimes renaming the Stacks and Notebooks do not automatically yield a sorted view. There is no way to force a sort as of now for the running session of the application. The only way to get the desired sorting in place is to close Evernote using File > Exit and then reopening it. While reopening Evernote automatically does the alphabetical sorting of the Stacks and Notebooks tree available in its local database. [ compare attached screenshot 1, 2 and 3 ]
screenshot 1 screenshot 2
If a notebook is removed from a Stack and moved out to the main tree, the notebook is automatically placed in a sorted order. In this case the names of the Stacks and the names of the Notebooks moved to the main tree would be consider by Evernote for the alphabetical sorting of the main tree.
[ see the screenshot 4 ]
If you rename a Stack again and want to force the re-sorting the Stacks and Notebooks in the main tree, the only option is to to close Evernote using File > Exit and then reopening it.
[ see attached screenshot 5 ]