If you are deciding to get down in the dirt with low level DirectX api coming from XNA, you are in for some shocks -- there is no content pipeline that you don't create for yourself, and so many things you take for granted in XNA just don't exist at the low level, so you'll be writing a lot of engine code if you are planning anything more than the simplest of demos... This is in fact what I've been involved with for the last couple of months... building an engine around SharpDX/DX11 in C#... Our team is coming out of an XNA/Unity background, and despite a lot of progress so far -- we don't have much beyond materials(shaders)/meshes/input/HUD implemented and tested at this point... physics integration is in progress and we have lots more engine features planned... but there is still a long way to go :)
If you want to keep to the more XNA level of abstraction you may want to look at SharpDX.Toolkit.. it provides and XNA-like interface but fully backed by DX11 instead of DX9 but doent have content pipeline support... If you are hooked on the content pipeline features then look at Monogame...
So if you do decide to play in the dirt, you can forget about XNB files.. you will be loading your mesh and texture data directly from the various model and image formats supported by the raw DX11 API, or integrating with a more capable asset library like AssImp (asset importer for C#)
I just read your OP a bit closer and it seems sort of like you are talking XML as data to drive the game... in that case if you stick with C#/SharpDX you can embed the XML as a resource in your assemblies and visual studio will handle rebuilding when you make changes. Short of knowing more about the language and API you are planning to use, there isn't much more I can say