Try looking at this thread:
Now, if you want to scan mail AS IT IS RECEIVED, I'm pretty sure you have to modify the kernel. Instructions are available in a file that comes with the Bitdefender download, as I remember. I've never done this because it's beyond my level of know-how. I just scan the mail folder daily (and I also update the virus databases daily).
Just set your cron job to scan your ~/.thunderbird folder and you should be all set.