Compiling an autotools project (or something else, prviding its own make-file).

[LonelySTar]

Hey together,
I have a autotoolset project, and I want to work on it using Codeblocks.
So I created a project, got to "Project-Properties" and selected "This is a custom makefile". I had to rename the target to "all", because otherwise compilation was started with "make default" (which does not work, but "make all" does). OK, I then had to move the project into the "src" subdirectory, because otherwise all "build messages" would contain the path "file.cc" and clicking on them did not open them because the real path is "src/file.cc".
Moving the Project file into the "src" subdirectory helped, but what do I do when I have a project with multiple targets in different subdirectories?
So far so good!
But now the problem is: When I do "Build->Build", firstly "make all" is executed. Fine! But then, it starts to build all files seperatly (they all are already build by "make all"). I don't want that! Can I switch it off?
Thanks!
Nathan