So, all my scouts do not show in the main map which results in my frequent losing track of them. Is there some kind of option to show scouts/assassins on the main map so I can keep track of them properly.
Currently I am using the Nation Overview in order to keep track of them but this is far more work than I think it warrants.
Just keep hitting the "n" key during your turn. This will automatically take you to every unit with "defend", "hide", or "siege" orders.
This way you can give each unit an order, and you know are you finished when it starts cycling back through the units that you actual want to "defend", "hide", or "siege".