Hi,
On the standalone, when you save the current settings (through File->Save Config), they are saved in ~/.rtabmap/rtabmap.ini. By default when opening RTAB-Map, the settings from this file are loaded. So yes, if you loaded another ini file, the parameters will be saved in ~/.rtabmap/rtabmap.ini (when File->Save Config will be clicked or "ctrl-s" in the main window).
In ROS, this is a little different.
rtabmapviz: its settings are loaded from ~/.ros/rtabmapGUI.ini by default. You can change the file (like with RVIZ config) using "-d config.ini" argument.
<node pkg="rtabmap_ros" type="rtabmapviz" name="rtabmapviz" args="-d config.ini"/>
rtabmap: Parameters can be set explicitly through rosparam or a config file can be loaded. By default, no config file is loaded. See "config_path" parameter.
<node pkg="rtabmap_ros" type="rtabmap" name="rtabmap">
<param name="config_path" type="string" value="config.ini"/>
</node>
Odometry nodes: Parameters should be set explicitly through rosparam.
I'll check to add "config_path" parameter to these nodes for convenience.
cheers