Hi!
Welcome aboard!
Each of this squares represent 3 units (beware: units, no elements. So both 3 leaders and 3 full divisions are one square )
The color have two modes:
- On the supply layer they represent supply level of the stack: red awful, orange bad, yellow so-so, green good.
- On all the other map layers they represent, as i understand, a mix between health and cohesion. As above, colors go from red (bad) to green (good).
On structures (cities, forts...) you will also see squares to represent the garrison inside the structure (the same: one square=3 units).
And blue squares represent naval units on structures with ports.
Regards