The Apache example should give you a feel for how Debian splits configuration files into smaller, more easily managed files, and provides means to ease various administration tasks, such as activating and deactivation modules. Other software will have different layouts, as well as, different configuration features and utilities, all described in the appropriate documentation.
Exim, for example, uses a single, monolithic configuration file. In order to split files out, Debian provides a utility update-exim4. conf that combines all of the separate configuration files from the / etc/exim4 / conf . d hierarchy into the single file required by the exim4 software. There are several minor variations in how this may be done (all explained in the documentation), so that an administrator can choose his preferred method.
Debian sendmail, another email package, uses another method. All of its configuration files are in the /etc/mail hierarchy, and GNU make is used after updating the configuration to create all of the necessary database and config files. In fact, a special utility, sendmailconfig, will not only run make for you, it will also handle incorporating /etc/default/sendrnail changes, and reload the sendmail configuration after processing is complete.
All of this shows how the Debian developers provide various methods of making configuration easier. Simpler packages may have few, one, or no configuration files. Those with larger or more complex configuration won't all be handled identically, although the technique of splitting files into smaller, easier to modify pieces and providing utilities to ease config administration will be common to most (and, per Debian policy, described in the documentation for each package).