Also, what would I use as a command line if I simply wanted to scan my
entire C drive:
"c:\program files\clamAV\clamscan" --temp=c:\windows\temp -i
--log="C:\Program files\Clamav\log\latestscan.log" C:\
Would that get what I need in terms of just showing virus infected
items, etc. but catch all the files on the drive?
Yes, except for any that may be hidden by "rootkits". That issue is
being dealt with.
You can watch for them with
http://www.sysinternals.com/Utilities/RootkitRevealer.html
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