On several occasions I've seen instructions that involve creating a new configuration and customizing some build behavior. I use an embedded platform (NetBurner) that has a tool chain and plugin structure geared towards using Eclipse's managed build process. In the image below I've used the Manage Configurations button to create a new configuration but as you can see the checkbox I need to uncheck has been disabled.
The key is to open up the C/C++ build section and use the Tool Chain Editor section as shown below. Change the Current builder: drop down to one of the choices that doesn't have the word builder, something with the word make usually works.
Then go back to the C/C++ build tab. Now we can uncheck that stubborn checkbox.