1. Global settings: inside %MAVEN_INSTALL_FOLDER%/conf/
This file is always used! And you should be aware about this in cases you will also take settings.xml in other way.
2. User settings: inside %USER_HOME%/.m2/
This file is optional. Any settings defined in the user settings take precedence over the corresponding global settings.
3. Command line: through --settings %SETTINGS_FILE_PATH%
If there is a global settings file, but in some cases you must use another settings file from command line, you should also override the global settings from command line with:
--global-settings %SETTINGS_FILE_PATH%
One problem I encountered if you do not do it so is related to mirrors. For example you can have in global settings file:
<mirror>
<id>myproject</id>
<mirrorOf>*,!myproject.releases</mirrorOf>
<url>http://myrepo/</url>
</mirror>
and inside settings.xml used through command line other mirror like:
<mirror>
<id>myproject2</id>
<mirrorOf>*,!mydependency</mirrorOf>
<url>http://myrepo2/</url>
</mirror>
and a repository with id = mydependency which must be resolved from a specific url repo (other than http://myrepo2/).
Because of the mirror in global settings mydependency wont't be resolved by its specific repo, but from the url http://myrepo/ (because of mirror rules) and it will not be found!