You can maintain the application component hierarchy in RSA6. There are options to create/delete/rename and move hierarchy nodes under the Hierarchy menu.
To transport a modified version of the RSA6 application component hierarchy you will have to manually add it to a transport by adding R3TR DSAA APCO (to transport the inactive version of the hierachy use R3TR DSAD APCO).
If the application hierarchy is in the $TMP package you first have to set it to a transportable package as follows:
If your application component hierarchy is assigned to local object then first you need to change the package.
Go to TCode: SE03
For Object Type Selection use: DSAA
Now change object directory from $TMP to the one being used in your project.
See SAP note 382471 – BW-OLTP-APCO: How do I transport it?
Also check OSS note 542454
See also: http://scn.sap.com/thread/228915