there exist many ways to do this... :-)
If you use LANDesk Package Builder, the following could do it:
SYSTEM CHANGES - Registry - "Apply to each log in user"
For batch files take a look on rhyous' doc here: How to use Registry Keys in a Batch File
(started by LANDesk of login script...)
Or try startasuser.exe, s. this thread: http://community.landesk.com/support/message/2452#2452
If you are using 8.8 in your distribution package is has an option to run an the logged in user. You can choose this on the accounts section. If you are installing software to users that do not have rights, this option will not work. For modifying HKEY_CURRENT_USER it should.