I like the tooltips because they allow me to find out what faction a boat, army or castle belong to if I'm not familiar with the colors.

On the subject of sorting out the armies, once my standing armies start getting bigger than one stack, I generally separate them into four groups: spears, swords, cavalry, and archers. This allows me to reorganize fairly quickly after a battle. It also makes it easier to figure out the composition of an army in each province. If I need to shift some troops to a province that just got hammered in a defensive battle, I can easily see if the surrounding provinces have a couple extra spear units or whatever. If you use this trick, just remember that the individual stacks will probably have 0 star generals, which is fine as long as there is a good general in the province in case of attack. You just have to make sure that whoever is the "general" for each stack has decent loyalty or you'll end up with a rebellion on your hands.