What is the best way to spawn preplaced and preshaped groups of enemies?

I'm titling each section with bold to make it readable, as Unity Answers likes to force you to write barely readable text walls, unable to make blank lines.

MY METHOD

• Place out enemies https://gyazo.com/24a3bb6764886a9dedd8f3a9b25bc801

• Make into prefab

• Load into serialized array on gamemanager script https://gyazo.com/0c15537add28d9e530cdeaf5501d760a

• Break apart prefabs and instantiate each enemy one at a time using this code: https://pastebin.com/p6vF1Bdb

THE PROBLEM WITH THIS

I'm making changes to these enemies all the time. Putting prefabs inside prefabs makes it so when I update the individual enemy prefabs, they're not changed inside the formations I already created. Also, maybe I'll want to reuse formations but with different enemies, and I can't right now without just recreating a whole new prefab.

WHAT I'D LIKE TO ACCOMPLISH: THE QUESTION

My main goal is to somehow be able to easily create formations like this by hand and be able to use them just as positions, as the method I'm using right now is just terribly clunky and hard to customize. How can I do this, and, possibly, how can I make my code better to accommodate that?

Thanks.