You can modify the CharacterControlsConfig.xml, CustomRigControlsConfig.xml, or FullRigControlsConfig.xml files 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 Character Controls configuration file is located in the CharacterControls directory: (C:\Program Files\Autodesk\<Maya version>\resources\CharacterControls). For more on CharacterControlsConfig.xml, CustomRigControlsConfig.xml, or FullRigControlsConfig.xml, see HumanIK Character Controls templates.
See Reposition effectors in the HumanIK Character representation, Customize the Custom Rig Character Definition background, and Save and load a new HumanIK Character Controls layout.