You can use the appropriate pkg-config call in the projects build-options ("Compiler settings -> Other options" for the includes and cppflags and "Linker settings -> Other linker settiings" for the libs).
Just add them included in backticks "`" and they will be automatically expanded by the C::B build-system.
To see how it works, you can have a look at a wizard-created wxWidgets project.
Example for gtk+-2.0:
`pkg-config --cflags gtk+-2.0`
and
`pkg-config --libs gtk+-2.0`