For now, I've decided to use Managed DirectX 9.0 for the project, instead of the previous thoughts of using X3D. The decision is mostly based on already using C# for the project, and therefore wanting to use this for as much as possible.
I haven't decided yet if it's better to open a new window with the DirectX content, but of course this is a simple technicality which I can wait with considering.
For anyone interested in learning Managed DirectX, I've only found one interesting book so far. There's a few sample chapters at Developers Fusion which seem interesting. However, there's a new book coming out soon, called Managed DirectX Game Programming, which should be updated with changes made to the SDK since. I've collected a few other resources (websites, articles etc.) regarding but wont publish links unless asked.