By default, the config.m4 file created by ext_skel accepts both directives and automatically enables your extension.
The default file creates two configuration directives in the configure script: --with-my_module and --enable-my_module. Use the first option when referring external files (such as the --with-apache directive that refers to the Apache directory). Use the second option when the user simply has to decide whether to enable your extension. Regardless of which option you use, you should uncomment the other, unnecessary one; that is, if you're using --enable-my_module, you should remove support for --with-my_module, and vice versa.