direction of the decking

[Elovia]

... only the lower deck with the railing has the room title of Deck. I am unable to select the upper deck, as a whole.

Can you select the room space for the upper deck in Plan View? If not, you have an error in enclosing the space. If you can select the room, be sure to define the space as a deck, and then use the advanced framing tool to remove the framing that you've already built; any extra pieces of framing left over should be selectable and deletable.

I was having problems with the lower deck, trying to connect the 2 levels with stairs. The stairs kept passing through the deck, to the ground.

I'm going to assume you're using the Click-Stair tool for this. I believe that you will need to make sure the two decks share a common wall (even if invisible), so that the software knows which two (adjacent) elevations to connect with stairs. If your two decks need to be separated by a gap (that the stairs will then bridge), temporarily build an invisible wall extension to the upper deck that also connects to the lower deck (be sure to set the correct elevation of the extension); then use the click-stairs tool to automatically build the stairs, and then manually drag the stairs over until the top of the stairs meets the visible deck edge.

Good luck.