When exporting your models, we highly advice checking your models in view3dscene to see if everything is exported correctly. Opening models in view3dscene is usually easier than running your whole game to test that a particular asset was exported OK. And view3dscene was implemented using our engine, so it can render exactly the same thing as your game.
The advised 3D and 2D formats to use are described on this page:
These pages describe the adviced approach for a particular authoring software:
The engine by default follows the convention that the Y axis is "up". This is also the recommended convention of both glTF and X3D. The exporters generally automatically adjust to it, e.g. when exporting from Blender (where the Z axis is by convention "up"), the exporter rotates your model. See "Which way is up?" manual chapter for more information about this, and how you can customize it.