Rowling draws the towers as only one circle, seen from plan view
Baring any sort of undetectable expansion charms, or who knows what magic, this would imply that indeed the dorms are stacked. This matches with the description of the dorms being on different levels than the common room and circular.
Rowling's hand-drawn map of Hogwarts
As a kid, pre-movie days, I would scour the books and the internet for more info on what Hogwarts looks like. However as @Rubenxfd stated, it's not clearly laid out in the books
Although it's mentioned Hogwarts changes, we don't see this happen much in the books from Harry's perspective. The layout seems fairly consistent. We don't see rooms flying all over the place.
I haven't drawn a [floor plan of Hogwarts], because it would be difficult for the most skilled architect to draw, owing to the fact that the staircases and the rooms keep moving. However, I have a very vivid mental image of what it looks like.
Rowling Scholastic Interview
I seem to remember there being canonical comments on this, but my memory could be wrong.
Also, we know that the girls' dorms are above the common room as well.
I don't have the books around, but when Harry and Ron go up the girls' staircase, it turns into a slide, and they slide back down. This tells us that the girls' dorms are also higher than the common room.
HP wiki, girls's dorm
Other sources, possibly non-canon:
Harry Potter Lexicon - Harry's Dorm Room
In-depth book-based analysis of Hogwarts