On the Enter Base Directory page of the Makefile Wizard, you specify the directory where you want the IDE to execute the make command.
In most cases the base directory is the location of both the makefile and the source tree. You can put your makefile in the base directory and your source files in another directory. However, if you do so, you can execute the make command on the makefile from the IDE only if you set the Build Directory property of the makefile to the base directory.