There are two actions to create an instance of a sprite.
1) System -> Create object (in the manual under System Actions)
2) <Sprite> -> Spawn another object (in the manual under Sprites/Sprite Actions)
Create object creates the instance at a location you specify.
Spawning creates the new instance at an imagepoint you specify on the spawning object. (For example, the bullet in the ghost shooter example in the Beginner's Guide to C2.)
When you create or spawn the object it is the current instance, so that is the perfect time to save its UID into your arrays, as well as to change other properties. In the case of a spawned sprite, you may also find it useful to save the UID of the parent object in an instance variable on the sprite. That way you can easily pick all of the "children" of a sprite and move or destroy them at once.
In both cases there currently needs to be an instance of the object in some layout in your project when the game starts running. You can delete it anytime after it starts. (This limitation may be removed at some later date.)
To delete an old sprite, select the particular instance of the sprite using some method of your choosing and use the sprite's destroy action.
As far as knowing how to procede, I'd suggest you do as many tutorials as you can stand at first, examine some of the example games on the arcade (the ones in the example category often have downloadable project files) and in the forum How Do I threads, and try recreating a few very simple games before you tackle something as ambitious as your project sounds. I think you'll save time in the long run.
If you're used to programming with code, Construct 2 is a little bit odd to work with at first (especially selecting instances of objects) but once you get the hang of it, it is a delight and makes for very fast development.