Themes files that are installed to the private folder of Skin Server are backed up/restored as a part of Skin Server private data. But if you want to make it visible in Application Manager and uninstall it after restore, this requires additional steps:
1- You need to create "backup_registration.xml" that has "system_backup" tag. The following is a sample content:
<?xml version="1.0" standalone="yes"?>
<restore requires_reboot = "no"/>
2- You need to update .pkg file and add the following line. <package UID> is your themes package UID.
"backup_registration.xml" - "!:\private\10202D56\import\packages\<package UID>\backup_registration.xml"
"backup_registration.xml" - "!:\private\10202D56\import\packages\a0000555\backup_registration.xml"