Just start changing the ini settings in the IGuidance.ini file.
It took me a little while to get the hang of it but now I have been able to embedd any program I can think of.
Only problem I have is sometimes when exiting an app the app itself will close but skinbedder will stay open. If you try and close it you get a string of errors and you need to ctrl-alt-del to end the skinbedder task.
My fix was to create an .exe with Autoit that killed the Skinbedder task, problem gone.
Here is a screen shot of a NES Emulator
I can send you the a modded ini or kill.exe file if it helps.