You should create your project in 3D, although it's only a minor convenience.
The two modes don't change any aspects of what your game can do or the fundamental workflow, they just configure certain defaults you can easily change as needed.
In 2D mode, images are imported as UI/Sprites by default, but if you're using 3D objects you'll typically want them imported as Textures instead, so having that as the default will save you a little settings fiddling.
The other difference is a 2D project will default to a 2D scene viewport, but you'll probably be switching this back and forth with the button on the scene window fairly frequently no matter which default you choose.
The directions of movement are determined by the script components you attach (like Rigidbody or Rigidbody2D) and you can access both 2D & 3D movement scripts no matter how you initially configured your project. Just be cautious you don't inadvertently mix them, as the 2D & 3D physics don't interact with one another.