You have to take the sprite of the summon spirit and place it on the grid (if the sprite can't fit in one box, just place it over multiple squares until you have room for it). Then, just color the background something (make sure the whole background is a solid color) and import it into RPG Maker.
If you want your summon to replace the caster (I don't know how to get rid of all the characters), then make a 1-frame long animation of the summon spirit (make sure the sprite is directly on the picture of the enemy that's in the animation editor), then go to "Animations 2". Click on the sprite that is the summoning character, then click "Animation Type". Click a blank slot on the list, then select the 1-frame long animation. You can change the name of the slot you picked in the "Poses" section. Then, you just set the skill's Animation (this is what your character looks like during the skill) as the summon, and set the Battle Animation (the summon's attack).
Finally, the "Battle2" folder is also for animations. These have a larger grid (the 640x640 images) and are used to fit larger sprites on them. Besides that, they're the same as regular animations.