Their only documentation shows what the xml config looks like but they don't give an example of how to load it so here is a simple example which shows both pieces of the puzzle.
Xml Config
This would be in a file called NinjectModules.xml. For it to find the type, I had to give it the assembly qualified name, even though everything was in a single .exe.
<module name="SomeModule">
<bind
service="Birds.IOwl, Birds, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null"
to="Birds.SlowOwl, Birds, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null"/>
</module>
Loading Config
IKernel kernel = new StandardKernel();
kernel.Load("c:\path\to\NinjectModules.xml");
IOwl owl = kernel.Get<IOwl>();
owl.Fly();