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The best way to manage overlays and .rosinstall is to use rosws instead of doing that manually.

In general, your method also works. The tools only simplify that.

Regarding the rqt_gui_cpp warning: This is probably, because you added the trunk. If you don't need the paramedit rosgui plugin, it is safe to ignore. Otherwise, there is ros-fuerte-rqt, which contains rqt_gui_cpp.