Let's make an example in Eclipse: I have two different source files for a Startup with a main-function, but depending on
 which build configuration I use, either one of them is used, or the other one.

I do this, by defining a custom symbol with the "-d" option in one of the build configurations, and leaving it out in 
the other one.

#ifdef CUSTOMSYMBOL
...
Specifically, under Eclipse, I can edit these settings under Project -> Properties -> C/C++ Build -> Settings -> Cygwin 
C++ Compiler -> Prepocessor imgdesc (I am using Cygwin under Windows for my C++ projects)

This works. Depending on which build configuration I use, only one of the two source files will be built by the compiler
 and the other one will be ignored.

However, this setting is specific to Cygwin.

I can't figure out, how to do it in QNX Momentics, since I do not have those options under the qcc Compiler.