Keeping track of units??

[Discoskull]

It's pretty easy for me to keep track of my troops/navies, since they each represent a substantial amount of money and time, and there are only one or two of them active on the map at any given time. As for diplomats and spies and the like...I keep at least 2 diplomats in each city and spies in the cities with large populations, as well as spies just sitting out in feild watching enemy/ally army movements.
The only agents I bother to keep track of are the extremely experienced/gifted/natrual born agents, which are the only ones I use for the agent-y stuff anyway. The others just sit.
You'll find that agents are much much more useful in EB, and they don't cost all that much in comparison to the military units, like they did in vanilla...

[Obelics]

you can just right-click on the labels "army" (for family members/captains/fleet), "towns" for settlements and "agents" for spy/assassins/diplomats

you can also sort the list by clicking on the title of the scroll that appear, that is very usefull...

[eadingas]

It also helps to have Ctrl+N on, this way you won't have to look for your armies and agents hidden on the map :)

[Davey]

Great info. Thanks guys!

[pezhetairoi]

You can always right click on your agents tab in strat map view to see a complete list of all diplomats, assassins and agents you own, and their location and attributes. You can do the same on the army tab to see all your military forces, units in transit and garrisons, their commanders, their locations, and their strengths.

Agent-wise I like to create a network of spies across my lands, and any lands I intend to invade or which seems to be attacking me. Hence I have between twenty and thirty spies spread out across my Roman Republic as mobile watchtowers, and ten diplomats in the same way. That way I don't have to worry about where my spies are because wherever I look or am, there will always be a spy on hand for me to deploy where I need him, be he deep in Arverni territory, or at the frontier with Makedonia.