Hello,
To answer your questions:
Can someone tell me what are the differences between the various feature sets?
Check these Articles which explains -
About Symantec Endpoint Protection
http://www.symantec.com/docs/HOWTO27254
About the types of protection
http://www.symantec.com/docs/HOWTO27250
More specifically, we run the Antivirus only scan but discovered that a client computer had malware on it (this malware actually deleted the contents of the Symantec folder on the computer hard drive). Does the antivirus feature set scan for malware?
Yes, Symantec offers superior anti-malware protection for PCs and all servers machines and removes more malware and scans faster than any product in its class.
Should I use the Antivirus and Antispyware feature set instead?
When installing the Antivirus Feature, it also provides Antispyware protection.
Also, check this Articles below:
Symantec Endpoint Protection 11.0 Frequently Asked Questions
http://www.symantec.com/docs/TECH102211
Symantec Endpoint Protection – Best Practices for Stopping Malware.
http://www.symantec.com/theme.jsp?themeid=stopping_malware
Hope that helps!!