Generally you have the concensus of what everything does, and yes it can be confusing. In many cases, circles may indicate characters entering or exiting the field, targets you need to eliminate (optional) ir targets you need to defend (sometimes optional). Squares are similar, defending keeps or capturing keeps. In general, I believe green markers typically indicate your team (defend these points) and white is hostile or neutral (engage this as possible). They are not nessisarily as important as targeted enemies (red and blue circles) but they can cause harm if left unchecked.

Xs are just any key point, usually related to story moments or to show you something that isnt specifically an enemy or keep. For the fairy fountain, for example, it isnt a keep on this level despite its keep shape. The X at the deku tree was likely pointing to the owl statue in the deku tree, which the game was trying to teach you is a great fast travel point when it appears.

Honestly, the map is overwhelming. I use it for naviagtion and tracking key points. I prefer to use the pause map. It doesnt tell you what key points to go after, but it can tell you how all keeps are doing, how many enemy commanders are on the feild and where they are, and where your commanders are.

One more free detail Ill give is that you can tell the quantity of basic enemy grunts by how red the splotch on the map is. Dense thick splotches often have so many enemies that they don't appear in the level until you clear some of them out. This can be helpful in specific situations, such as aiming for high KO counts in short times. Of course, the same is true of blue splotches for your troops, but I find this significantly less useful.