This is really a question about Notification Server site maintenance behavior rather than Agent behavior. See article 2397 for more information on site maintenance. The Altiris Agent always downloads from the codebases that are given out by the Notification Server.
New in Notification Server 6.0 SP2 is that the Notification Server no longer hands out its own codebases to agents that are members of a site; this change was due to a very common customer request. To compensate for this change in behavior a new CoreSettings.config item was created and is disabled by default (meaning agents will strictly adhere to the site maintenance configuration):
The agent now will send a running time value to the server when it makes its calls to GetPackageInfo.aspx on the Notification Server. When this time value exceeds the MaxAgentDownloadTryingTimeMins value the Notification Server will hand out its own codebases in place of the codebases of any Package Server within the given site. Please note that this is a global setting, and cannot be configured for individual sites.The preferred method to implement MaxAgentDownloadTryingTimeMins on the Notification Server is to use the NSConfigurator. The Notification Server 6.0 SP3 release notes, section 3.1.25, provides information on how to install and use the NSConfigurator (see article 19106).