It’s never been possible for moderators to set sub-specific CSS through the redesign, outside of sidebar widgets.
The official line is that this capability will be added after everything else has been implemented. Given how much other functionality is missing, this looks to be a long way down the track.
Users will still have the option of switching back to the original design, where your old CSS will still function. You won’t have any way to choose which version of the sub your users see.