If you are using Unity, you don't need to prepack all your parts.
You can use Spine-Unity's Mix and Match workflow, as well as pull images from Unity Sprites.
Spine-Unity Mix and Match
But it's a very specific way of setting up your skeleton. If you already did a lot of work, this may be even more work.
But it'll be less work down the line if you need to add more customization.
If you have many but not that many customization options, you'll probably be better off with a prepacked atlas like you are already doing.
Additionally: If you are using Spine PRO, it's better to remove all those empty spaces from your images before using them in Spine. You won't be able to strip them automatically in case you need to use them on meshes on your skeleton.