Webmin understands the configuration file layout of many distributions. The main problem is when a particular module does not handle certain types of configuration in the way the Debian developers prefer, which can make package upgrades somewhat difficult.
This can be handled in a couple of ways. Most modules provide a means to edit configuration files directly, so if you have read the Debian documentation you can modify the configuration appropriately to use Debian specific configuration techniques. Or, you may choose to allow Webmin to modify files as it sees fit, and handle any conflicts manually when you upgrade the software involved. Finally, you can avoid those modules involved with specific software that are more likely to cause problems.
Webmin modules are constantly changing, and some actually recognize the Debian file layouts well, so it is not possible to give a comprehensive list of modules to avoid at this time.
Best practice when using Webmin is to read the documentation and check the configuration files for specific software prior to using Webmin. Then, after configuring with Webmin, check the files again to determine whether changes may be required to work within the particular package's Debian configuration framework. Based upon this, you can decide whether to continue to configure using Webmin or switch back to manual configuration of that particular software.
