If the full scan really is a full scan, then every single file on all your partitions should be scanned, regardless of what program uses it. Otherwise it's not really a full scan is it? Most AVs have a certain amount of options regarding how much is scanned; compressed folders, system files, etc. Tick all the relevant boxes and it should be fine.
I don't use Panda, so I'm not overly familiar with it, though I do know that it is one of the few AVs that can scan at a root level. So you're lucky, given the recent rise in rootkit-based malware.
As for on-the-fly email scanning as messages arrive; that is generally much more limited, usually to Outlook and Outlook Express. Users of Thunderbird, etc. are not guaranteed full compatibility. That one depends on the AV.