what is the difference in behavior of manually installed SCOM agent and discovery wizard installed SCOM Agent?

Hi

There is no difference in functionality as far as the actual agent is concerned.

The difference is that if you push the agent from the console then you can "remotely manage it". You can go to Administration, Agent Managed and move the agent to a new Primary Management Server. You can also update the agent from Pending Management.

Manually installed agents need to managed via PowerShell (Primary \ secondary management servers) and also manually updated.

There is a good explanation here:

http://blogs.technet.com/b/kevinholman/archive/2010/02/20/how-to-get-your-agents-back-to-remotely-manageable-in-opsmgr-2007-r2.aspx

The comments at the bottom are also worth a read.

Regards

Graham