You can modify the CharacterControlsConfig.xml or CustomRigControlsConfig.xml file to adjust the Controls or Custom Rig character layout. When modifications are complete, you can save your customized file in a location of your choice, before loading the file in Maya to view your new layout.
The following image shows the default layout in the Custom Rig tab. The configuration file has not yet been edited. 
The following image shows the Custom Rig layout for the same character after some simple modifications to the CustomRigControlsConfig.xml file. 