Hi,
Thank you for posting in Symantec community.
In case you are not awere SEP 12.1 RU4 is the latest release.
You should plan to upgrade to SEP 12.1 RU4 insteasd of SEP 12.1 RU3.
Autoupdate can update the SEP client version though anyone is not logged in.
Note: You must test the AutoUpgrade process before you attempt to upgrade a large number of clients in your production network. If you do not have a test network, you can create a test group. You can add a few non-critical clients to the test group and upgrade them by using AutoUpgrade. You can confirm the upgrade completed successfully by verifying the version number of the client software that appears in the About dialog box.
It's always recommended to have Symantec Endpoint Protection Manager and SEP clients on the same version.
Public Kb:
Upgrading clients by using AutoUpgrade
http://www.symantec.com/docs/TECH96789