I believe you are looking for IModelViewManager::CreateFeatureMgrWindowFromHandle.
Here is an example of loading a .net control from the documentation.
Thanks for the suggestion. I've already played with that and can successfully create feature manager tabs but that doesn't seem to be tied in any way to the model control tabs (at the bottom). None of the examples or API that I've seen is able to reproduce the behavior of the Simulation plugin.
The desired behavior is as follows (note the "Static 1" control tab at the bottom and its corresponding window (with a tree) right under the feature manager windows - the splitter position is 0.0 in this case but it can be changed so that you would see two feature manager trees above the simulation specific window):
And what the DisplayWindowFromHandle functionality produces is something like this (note the added control takes up a large part of the window at the bottom and there doesn't seem to be a way to adjust the splitter off that window using the API - this is a different splitter from the one between the freature manager trees):