You copy the spell or ability for every permanent or player it could target. That is, you don't choose either permanents or players and then make copies based on that.

You control all the copies, and you'll choose which copy targets which permanent or player. For example, if the original spell says, "Destroy target creature," you'll ultimately choose the order in which each creature targeted by a copy is destroyed. Remember that the original spell or ability will resolve after all of the copies.

Each copy you create will cause your magecraft abilities to trigger.

You can choose a spell or ability with multiple targets as long as all of those targets are the same permanent or player.