The Geospatial Administrator does not provide options for customizing the Command Manager. For example, the following are the results of running the Update Command Manager List tool.  Note that the Place and Promote entries are placed in the same category as the feature which may not be desired.

A quick and easy method to reorganize the Command Manager is to select all rows and press CTRL+C to copy the contents to the system clipboard.

Open Excel, or a similar spreadsheet program, and do a CTRL+V.  Then proceed to customize and re-order as needed.  When done, select the rows in the workbook and copy to the changes back to the system clipboard.

In the Geospatial Administrator, select all of the rows in the Command Manager tab and do a CTRL+V to paste the customized list of commands from Excel.

When exported, the Command Manager will reflect the changes.  In this example, all of the Promote commands were put into their own category for simplicity. 

Note:  Another method of customizing the Command Manager is make the changes directly inside MainMenu.xml using any text editor.  While this might work for you, keep in mind that the file will be written over the next time the project is exported from Geospatial Administrator.