You use a Makefile-Project. Everything that has to be done, including where to put an executable, has to be coded into the Makefile by you! Eclipse just kicks the build by invoking make.
An simple example:
CXXFLAGS= -g -O0
CXX=g++
all: bin bin/test
bin/test: bin/test.o
$(CXX) -o bin/test bin/test.o
bin/test.o: test.cpp
$(CXX) $(CXXFLAGS) -o bin/test.o -c test.cpp
bin:
mkdir bin
clean:
rm bin/test.o
rm bin/test
This is the source I learned how to write a Makefile from: http://www.eng.hawaii.edu/Tutor/Make
Plain Makefiles are handy for projects with a small number of files. Once you've been bitten by having a segfault due to missing recompilaton (forgot to list a header file at the .o: dependencies) you should move on to a full blown build system, like cmake. cmake generates Makefiles for you, but its important to understand the fundamentals of Makfiles to interpret error messages.