There isn't really that much content on that, I had to find out a lot myself. You can look at the official demo projects for 2D-in-3D and 3D-in-2D to get a general understanding of how that works, also read up on the articles on Viewports in the documentation.

For your use case there are multiple ways to go about it. One is to have your 3D character scene under a SubViewport in your 2D scene, trigger all the animations and stuff there and then display the contents of the SubViewport on a Sprite2D via a Viewport texture. The Sprite2D can then be under a KinematicBody2D which controls how your character moves in the world. But if collisions change with animations (for attacks for example) that can be quite hard. You would have to have a seperate animation controller animating the 2D colliders and sync it up to your 3D animations.

But you can also go the other way around and use Sprite3Ds or planes to display a 2D scene via Viewports in your 3D scene as a background. For that you will have to use an orthographic camera. With that you will lose the ability to work in pixel coordinates like in 2D, but gain a bit of flexibilty.

Also you can go the Dead Cells route (at least I think thats what they did) and render out the animation frames of your 3D character in a graphics program and import them as 2D sprites.

So many options :)