Menu items created by programs are stored in /_config/programlinks.cfm. You can edit the XML here to change the order, labels, URLs, or hierarchy of the admin menu links.
Here is an example of a programlinks.cfm file
<site>
<program name="Admins" path="/admin/admins/" />
<program name="CMS" path="/admin/cms/">
<link label="Pages" url="page-list.cfm" />
<link label="Sections" url="section-list.cfm" />
</program>
</site>
The information here could be extracted by calling Application.Framework.getProgramLinksArray(). For the above example, this would be the result:
This links will often be created by the links method of Program.cfc. For example, the CMS entry from above could have been created by the following "links" method:
<cffunction name="links" access="public" returntype="string" output="yes">
<program permissions="CMS">
<link label="Pages" url="page-list.cfm" />
<link label="Sections" url="section-list.cfm" />
</program>
</cffunction>
If you are using the default generated code, then the layout will pass this information to cf_sebMenu to populate the links of your administration section by passing the results of Application.Framework.getProgramLinksArray() to the "data" argument of cf_sebMenu.