How can I run Tomcat with maven:run with my custom configuration file?

I want to run my Tomcat project by mvn tomcat:run

In which path can I put my tomcat-user.xml to load it dynamically ?

Use the tomcat-maven-plugin, it has configuration for this.

See http://mojo.codehaus.org/tomcat-maven-plugin/run-mojo.html#additionalConfigFilesDir.