I have installed CLAMAV on my first CENTOS 6.x server. It is up and running and freshclam and the scan are both scheduled via CRON.
Right now, I am only scanning the /home directory.
Which directories should I scan? How can I scan more than one directory in a script?

Here is my code snippet for scanning the /home directory.

clamscan /home -r \
--move=/var/log/clamav \
--log=$LOG_FILE

If you are using Clam AV on a Linux-based computer, we can not provide any help here. Our forums are devoted to the use of the ClamWin open source antivirus program for Windows-based computers--from Windows 8 up through Windows 10. The ClamWin developers prepare a Windows port from the Clam AV Linux source code. ClamWin uses the Clam AV scan engine and virus signatures and is operated via a GUI by the user. It is primarily used on individual computers with some use on small networks.

I suggest you contact the Clam AV project for assistance.

Regards,