Empire Tree 101
At the top left of the screen is a push pin icon. This icon pins the said gravity well, ship, or structure to the empire tree. The default setting is each planet is pinned along with capitol ships and starbases. I keep this clean!! I I turned off the setting in the user interface options window that auto pins planets to the empire tree. You can instead de-pin every planet if you prefer on your own, but that is a major time sink. I also de-pin each starbase since I often have multiple of them. This leaves only the capitol ships pinned which makes for ease of seeing whats going on with your battlegroup.
(Do not forget to set your frigate factories as a group. I make frigate factories grouped as control+0. This way im not struggling to try and zoom out to click on the planet that has the factory in it. I just hit 0 and then build what i need.)
Next, ships traveling in phase space have their own spot on the empire tree. When they jump they appear directly under your fleet icon and disappear again when they exit phase space. This tends to make the empire tree skip around which is a major pain in the ass when you are trying to micro a battle. Since you cannot de-pin this carrot MAKE SURE TO MINIMIZE IT (can only be minimized when something is actually in phase space...so minimize it on your first phase jump to your roid), it will keep it that way until you start the game again after a save or start a new one.
Another useful thing to use is the stacking button located to the right of the pin and search buttons. Clicking this will change the fleet from stacked to unstacked. Be aware this will make your empire tree fill up qickly but is important to be able to micro ship abilities since the computer is not always the best at it. If you de-pin things as I have stated above you will have almost enough room to see an entire fleet.
If you have more that one fleet with capitol ships in it....you can click the carrot of the planet they are at to close the planets tree so that you will again be able to see the main fleet by itself. This is especially needed when the Advent are in combat with you and they have 5 or more guardians and they activate the "you cant see crap ability" which for some reason the developers have yet to find some better graphical representation for the shield share.
Clicking once on your empires icon at a specific gravity well will select all the combat ships present. Clicking again will select all strike craft. This is useful if you need to suddenly give orders to all SC at a specific gravity well (say to kill off the 40 some odd torpedo cruisers the computer is sending in to rearrange the face of your starbase).
That's all I can think of atm, hope this helps.