As of Embedded Coder R2014b, F28069M is not supported and there is no update to be downloaded to have this hardware show up in the menu.
The supported list is mentioned here: http://www.mathworks.com/help/supportpkg/texasinstrumentsc2000/ug/coder-target-pane-texas-instruments-c2000-processors.html?
Now, in order to assign memory differently, there is a good link explaining the workflow: http://www.mathworks.com/help/supportpkg/texasinstrumentsc2000/ug/programming-flash-memory.html?
Thanks Sandip Kumar MathWorks