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
Object: APCO
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