Instead of editing the deep project file manually the settings can be altered by choosing Project → Properties. Alternatively you can press the right mouse button on the project name in the package explorer:

Refactoring is a very powerful tool in the eclipse framework. You can rename a deep project by choosing a project in the package explorer and pressing Shift+Alt+R. The project together with its associated deep project file will be renamed.

All the run configurations of all projects in a workspace can be edited with Properties - > Run/Debug Settings.

With Run/Debug setting you can choose which run configuration of the chosen board you want to run. All the available run configuration (must be defined in the board description file) are listed. One of them can be chosen.
Within a run configuration you can also specify where your program will be written to. This can be RAM or flash memory (see Flashing your Program).