About spy swarming: it doesn't work in enemy provinces anymore since VI, but it increases loyalty in your own.

Inquisitors raise zeal until they start burning the populace, but keep them occupied with burning generals and they are not as likely to do so. I understand the the presence of a bishop or cardinal slowes down inquisitors but I am not sure if this applies to 'inquisition of individual'. Anyway, in my case the bishops and cardinals rose the zeal so high that the Papal Grand Inquisitors could fry a general every turn. The only thing that kept them from staying permanently was my horde of Syrian assassins watching around for people with odd-looking hats.