If you create your own sakai.properties file the standard place to locate it is $CATALINA_HOME/sakai. This directory is not created by Maven during the build and deployment process, so you will have to create it manually.
You may find it preferable to store Sakai's configuration files outside of the Tomcat file hierarchy. In a development environment, for example, you may find yourself frequently reinstalling Tomcat and unless you create a build script to automate the Tomcat installation and configuration process you will likely want to avoid having to recreate the $CATALINA_HOME/sakai folder and its property file contents each time.
To locate your properties file outside of Tomcat modify the Java startup command or the JAVA_OPTS environment variable and set a system property named sakai.home. Make sure your external location is readable and writable by Tomcat.
-Dsakai.home=/path/to/desired/sakai/home/