Question: We have an existing C++ project that is developed with eclipse. There is also a gui that is developed separately in Qt Creator.

We want to setup the eclipse project so that the gui is a sub-directory in the main project. The idea is that most of the gui development is done in Creator, but the entire project (including gui) can be built from eclipse.

I'm having trouble setting this up as a makefile build. I think I need to use eclipse' external tools to run qmake before building the project. The problem is that this creates the Qt makefile in the 'gui' directory and then eclipse doesn't see it.

Answer: 
This is how we ended up configuring this.

We have two build configurations, one for the main part of the project and one for the gui. For the main project, we exclude the gui from the build, and for the gui we exclude everything else but the gui from the build. The gui is build using a custom makefile that has targets for calling qmake and make. From QtCreator we just call "build" which runs the makefile, so qmake is never called from QtCreator.

It's not ideal but it works. The main drawback is that you have to switch build configurations in eclipse depending what you want to build. If I was setting it up again I'd make two different projects instead of two different build configurations in the same project. This way it's easier to manage the dependencies between the main program and the gui.
Indeed, you need to use the external tools. Add these in there: "qmake -project" and "qmake". The former is obviously not necessary if you have project file(s) already in there. You can then set the working directory, and arguments like the project file.

Then you can just run the externals tools from the menu. I am not sure what you mean by "Qt makefile" and by "Eclipse not seeing it."