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 Character Controls configuration file is located in the CharacterControls directory: (C:\Program Files\Autodesk\<Maya version>\resources\CharacterControls).
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.