Hello,
Questions and Answers -
1) What is the major difference between Sonar and auto protect?
Check this Article:
https://www-secure.symantec.com/connect/articles/information-symantec-endpoint-protection-scans
2) what are the type of threats that SEP Endpoint protection treats
All type of Malwares.
Security Best Practices for stopping malware and other threats
http://www.symantec.com/theme.jsp?themeid=stopping...
3) Is that SEP Endpint protection is compatible with System center 2012 Endpoint Protection?
Running more then one antivirus program on the same computer is not recommended. You may experience a false positive detection in one of the antivirus programs in this situation.
Risks of using more than one antivirus program
Antivirus and antispyware programs are generally written with the expectation that they will interrupt actions taken by other programs, in the interest of security. If more than one such program is running, there are a number of ways in which they can interfere with each other.
To give a simple example, suppose that antivirus scanners A and B are installed on a computer. Program A copies a file to a temporary location for scanning. Program B notices the file activity, and copies the file from program A's temporary location to its own. Program A notices that file activity and makes another copy, and so an infinite loop forms. This could end with the computer running out of memory or hard drive space, hangs or crashes in the antivirus scanners, or other undesirable behaviors.
Check this Article:
Should you run more than one antivirus program at the same time?
http://www.symantec.com/docs/TECH104806
4) I just noticed that when i have installed System center 2012 End point protection, it detected many virus that SEP haven't detected. How can you explain it?
You may be interested in checking these articles:
What to do when a competitor's antivirus, adware scanner, or spyware scanner detects a threat that Symantec AntiVirus does not detect
http://www.symantec.com/docs/TECH99494
What to do when you suspect that a Symantec AntiVirus product is not detecting viruses
http://www.symantec.com/docs/TECH99222
Using Symantec Help (SymHelp) Tool, how do we Collect the Suspicious Files and Submit the same to Symantec Security Response Team.
https://www-secure.symantec.com/connect/articles/using-symantec-help-symhelp-tool-how-do-we-collect-suspicious-files-and-submit-same-symante
Could you please zip each of those files detected by Third party Antivirus and submit the zip files (without password) to the Symantec Security Response Team on :
https://submit.symantec.com/websubmit/essential.cgi
We also offer a self-service site to analyze files, at http://www.threatexpert.com, which can give you more information on the files you submit to it.
Hope that helps!!