Basic process: render your character animations from TB with an alpha/transparent background, import those animations into your 3d scene in Blender on a flat plane (import as planes plugin works best with transparency turned on). Make sure to select the plane, and open the material node editor, and open the properties (N) in the node editor. This is a known work-around to the issue that animated textures will not animate in the viewport while scrubbing unless the node editor properties is open and the plane selected (hopefully this will be sorted out by version 2.8 ).
Then position the plane in your 3d environment. The compositing environment in Blender is far more capable than Toonboom’s, so use the built-in compositor and the 3d scene to create the final comp and animation.
You would also add background plates in the background at varying depths to create a nice looking parallax background. Be sure to match these with your camera angle(s ) when you draw them.
In your posted example the girl animation would be imported on a 3d plane, and placed in the 3d boat, and parented to the boat. The parrot animation would be animated in TB as a flat animation (without any zoom effect ), and again imported as a flat plane. Then animate the flat parrot plane flying through 3d space.
You do have to make sure your TB animations are rendered at a sufficiently high resolution to maintain final output resolution quality. You cannot import a 100x100px parrot animation, and animate it in 3d space towards the camera at 4K resolution and expecting it to hold up in regards to resolution: it will become a blurry pixel mess once it comes too close to the camera. This, make absolutely certain to plan out in advance what resolutions you will need. Luckily TB works in vector, so you could always do a simple test frame to check if the resolution is sufficient.
And plan, plan, plan ahead. Each 2d animated element must sync with the 3d elements.