A Level X is considered to be the same stage as the card it leveled up from. In the deck, it is a Pokemon card. No stage, not a basic, not an evolution, just a Pokemon. While in play however, The Level X takes on the characteristics of the card it did level up from.
Palkia X is a Basic
Dialga X is a Basic
Garchomp X is usually a Stage 2
I have to say usually, because of Garchomp X's attack, which can place a stage 2 onto your bench, as an basic, meaning you could in theory have a basic Infernape X.
Hope this helps!
~Duke