Not sure how much flexibility you're looking for on this but if you just want your whole touchgfx project to be in a subfolder of your existing project you can do that. This is how I have the current project I'm working on setup. You can still open the project in the designer and run the simulator assuming the simulator's build doesn't need any resources outside of this subfolder since its makefile won't have all the include paths yours does.
EDIT: added missing screenshot
