Can you debug a simple console project which uses the C::B's build system?
I've not tried these, but I think you need to make sure that
1. You have a compiler selected for your project (it would not be used for building, but it will be used for other stuff)
2. This compiler must have a working debugger configuration selected
3. Set the host app path to be the path where your executable is generated by your makefile
4. Setup execution directory in the Project -> Properties -> your target
2 is important only if you have "Debug -> Active debuggers -> Target's default" selected.