Yes, I use editor and write necessary XML nodes... This is _without C::B_ (unfortunately) =(
Please show me the nodes you are adding / modifying manually and I show you where the UI counterpart is. As I said: *All* settings are available via the UI options.
I created project under windows.
Moved from common part of .cbp to windows target this text:
  <Add option="-mthreads" /> 
  <Add option="-D__GNUWIN32__" /> 
  <Add option="-D__WXMSW__" /> 
  <Add option="-DWXUSINGDLL" /> 
  <Add option="-DwxUSE_UNICODE" />
...
  <Add directory="$(#wx)/include" /> 
  <Add directory="$(#wx)/contrib/include" /> 
  </Compiler>
- <ResourceCompiler>
  <Add directory="$(#wx)/lib/gcc_dll/mswu" /> 
  <Add directory="$(#wx)/include" /> 
  </ResourceCompiler>
- <Linker>
  <Add option="-s" /> 
  <Add library="libwxmsw28u.a" /> 
  <Add directory="$(#wx)/lib/gcc_dll" /> 
  </Linker>
And some other windows-cpecific parts...
Then I created separate project in Linux and moved Linux-specific options from this additional project...
- <Compiler>
  <Add option="-g" /> 
  <Add option="`wx-config --cflags`" /> 
  <Add option="-Wall" /> 
  </Compiler>
- <Linker>
  <Add option="`wx-config --libs`" /> 
  </Linker>
So, as you can see, if project creation wizard creating project it makes it NON-crosplatform... You need manual editing, and it is NOT convenient and not acceptable for many developers, it's ok only for me...
AND even if you can do this in c::b GUI, I think it is not normal to do this manually, this must be done to be automatically...