1. Companions can be seen in the screen where you equip items. Each can hold up to four items, and provide other benefits unique to the specific companion. For instance, once you heal his scars, Jimmy Kraud increases your leadership by 700.
Companions are not units and will not be seen on the battlefield.
2. I believe you're referring to reserve slots. You have five army slots for battle, and two reserve slots. Troops in the reserve slots do not participate in battles. You can swap out troops between your army and your reserve slots prior to battle, but once in a fight, you only have those troops in your army slots.
The primary purpose of reserve slots is to give you a bit of flexibility in which troops go into which fights. For example, if you have royal thorns, you may want to put them in reserve if going into a fight against imps, which throw around fireballs.
Another use is to tweak the strength of your army, as your pet's experience is dependent on the relative strength of your army vs. the enemy's. The stronger the enemy is relative to you, the more experience your dragon gains for using various abilities. Say I have four red dragons. For a weaker fight, I may take in only one, putting the other three in reserve. For a strong fight, I may use all four.
Don't get too discouraged. Pretty much everyone struggled with their first game, as some strategies are not obvious and require some experimentation. Once you develop the tactics that work for you, things will get much easier (one tip: you're almost always better off with a few higher-level units than lots of weak units).
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