Something most people know, but should be mentioned: On the campaign map, pressing the Z key will show agents only. Pressing it again will show armies or stacks only. Pressing it one more time will bring both unit types back on the map.

Also, pressing C will toggle fortifications on and off.

I like to clear the display of armies and cities once in a while, especially when playing Catholics, to keep track of agents -- especially inquisitors.

Frankly, I hate them. However, I don't pursue them to the death. They'll usually leave the province if all you do is assign an assassin to them. I keep high-valor assassins in all border provinces, especially ports, and attack inquisitors as soon as they cross my border.

The AI cheats. It knows when a contract has been put on one if its agents. It then moves that agent somewhere like a friendly province to drag your assassin through a border fort.

I don't see any good point to losing assassins once I've scared off the inquisition, so I break off the chase -- once they leave.