These are perhaps not secrets, but I am one of those who never read manuals. Even if you read it, you might very well forget many of the commands...
I don't know how long I played before I found out how to redeploy troops. (Select troop -> Hold down CTRL -> Right click on the province you wish to redeploy it to, must be land connected).
It is possible to group troops just like a RTS game. Select one (or many!) divisions and then press CTRL+1. It's very useful for fleets and finding your favorite troops.
Select your grand fleet, press CTRL+1 to bind it to that key. To quickly find you fleet, double press 1 on the keyboard.
Another thing I know some people get annoyed at is finding the country to do diplomacy with. Instead of finding the country in the list, you can click on a province that belongs to that country, then click on the flag on the top left part of your screen. It will open the diplomacy window.
If you want to use spies, then select an enemy province first, and then click on the intelligence tab.
(I just noticed right clicking on enemy province brings up the menu for intelligence and diplomacy as well)
Press ? to seach for provinces can be useful sometimes.
To press ? on some keyboard, you must hold down shift and click on the +, so it's not that obvious.
I wish someone could tell me a secret how to deploy all troops with only a couple clicks.
