I dont quite understand what you mean.
If you look at the Directories->Compiler tabs (in compiler options), where you put the include dirs, you see there are some arrows (I forgot the real name of that widget
). The compiler will try to look for headers (or libs, if in the Directories->Linker tabs) in the given order, so you can use the aforementioned arrows to change the precedence of such dirs (which one will be looked for first, second, and so on).
In the case of having two dirs, one in the global compiler setting an another in the local project compiler settings, my bet is that it searches for the local settings first and then tries to look at the global settings.
Is this what you're asking?