Edit:- Norm and I posted at the same time hence a lot of what I have said is a duplication.
The method you have used is CSG (constructive Solid Geometry)
See wiki pedia here
http://en.wikipedia.org/wiki/Constructi ... d_geometry
You can use this method if you want to but it has limitations. In FreeCAD there are usually several was to achieve something.
You said you wanted to make the position of the "cut out box" have a position constrained to the centre of the face of your First Box, hence I suggested you use the PartDesign workbench.
The assembly workbench will eventually be able to position items in 3d space with constraints relative to each other, but Assembly is still in early development and is probably going to be reasonably complicated.
In your very simple example the power of sketcher may seem less obvious, however imagine you cut out box were to be some odd shape rather than a regular shape. For example, sketcher could pocket using a star shaped cross section.
CSG in CAD can just mean using a CSG method with the GUI as in FreeCAD however it is also possible for it to be how the CAD software works behind the GUI. Some old fashioned CAD applications work that way, like BRLCAD. But it has limitations. FreeCAD is based on a more modern CAD kernel which uses BREP.
BREP see wiki pedia
The following quote is from Wiki pedia, in the page linked to above
Compared to the constructive solid geometry (CSG) representation, which uses only primitive objects and Boolean operations to combine them, boundary representation is more flexible and has a much richer operation set. This makes boundary representation a more appropriate choice for CAD systems. CSG was used initially by several commercial systems because it was easier to implement.
OpenSCAD according to its founder is only supposed to be a quick and simple utility, which presumably is why they based it around CSG. There is nothing wrong with that, it is great for what it was intended for.
OpenSCAD can be used within FreeCAD. There is file export/import which by its very nature will always have some limitations. Also you can actually run OpenSCAD from right inside FreeCAD. See the FreeCAD wiki on how to do that. Basically you have to install OpenSCAD and then tell FreeCAD where to find OpenSCAD on your computer and then go to the OpenSCAD workbench in FreeCAD.