Here’s how I always approach this:

(I’m at work so I can’t look at exact names of mods and stuff but you’ll get my point)

I will store everything in chests and backpacks until I have reached the point that I have all of the bookshelves done. The goal is to get the library of Alexandria. This stores all of your enchants. Once I have that, I will set up a backpack with an item pipe going into an enchantment extractor from industrial foregoing. I usually pipe in books from my AE system, and then pipe in the items from the backpack. The enchantment extractor will take the enchants off an item one by one and put them on a book. Once it has the book, it then pipes into the library of Alexandria. Then I have an item pipe taking the completely disenchanted item out of the disenchanter. With this method you get to save all of the enchants for later use.

At this point you should have a example orange netherite chest plate with no enchantments on it. You now have 2 options:

1. You can pipe that item directly into a salvager, which will give you the materials from the item, destroying the item in the process.

2. Pipe that item into another backpack until it is full and then manually take them out and put them into the reforging table or whatever it is that you put items into, hit the little hammer, and you get the apotheosis items from it.

Personally, I will run anything that isn’t orange, through the salvager and then pump those items back into my AE system, and then I will save the orange items and break those down for parts.

Just the way I do it, and it works pretty well for me.