You deal with Skins in v4.6 same way as in v4.5

Precisions:

How to proceed :

the various sections of configuration of the "look" of your Website were joined together in a common zone (Skin Configuration)

What you must keep in mind is that you can modify only the skin that is selected

In other words, if you chose "Original skin" in your preferences, you will modify only that skin in config site (Default skins theme: ).

It will be the same for the boxes configuration , you can reorganize only boxes for the current skin !

Thus: if you wish to modify another skin than the one selected in your Default skins theme you will have to select this other skin during your modifications .

Don't forget to generate the style sheet of your skin. The you can update that based style sheet if needed, or generate again a new one.
Generally we need to modify rights for the config flies (see chmod).