Let's take for example the recipe to make an LV circuit while in the stone age. You have the following "nested layers" in the recipe, so to speak:

Layer 1

• Crafting the LV circuit (2 resistors, 2 vacuum tubes, 3 red alloy cables, 1 circuit board, 1 steel casing
  Layer 2
• Crafting the resistor (2 slime balls, 2 fine copper wire, 2 copper wire, 1 coal dust)
• Crafting the vacuum tube (2 fine copper wire, 3 copper wire, 2 steel rods, 1 red alloy bolt, 1 glass tube)
• Crafting the steel casing (hammer + steel plate)
• Crafting the circuit board (8 copper wires, 1 coated circuit board)
• Crafting the red alloy cable (1 red alloy wire, 1 rubber sheet)
  Layer 3
• Crafting the copper wire (wire cutters + copper plate)
• Crafting the fine copper wire (wire cutters + copper foil)

etc. etc.

My suggestion would be to add a button which automatically sorts the order of recipes within a linked group / page based on:

• Nested Layers (inverted option available)
• Raw Materials (inverted option available) {aka items which are highlighted green when holding shift over a linked group/page}
• Maybe alphabetical w/inverted option

This to give a bit easier organizing for your NEI bookmark pages without having to manually move things around and potentially risk messing up a bookmark.

For specific clarity on "Nested Layer" vs "Raw Materials":
Nested Layer sorting would be based only on crafting layers. So in the above example, the "steel casing" craft would be with "layer 2" crafting recipes in sorting.
Raw Materials sorting would be based on crafting layers and whether the materials within a recipe are designated as "raw materials" (i.e. when highlighted "green" when holding down shift on the linked group/page). So if Steel Plates would be considered a "raw material", it wouldn't be part of Layer 2. Rather it would be listed at the bottom/top (dependent on inverted sorting) with the other raw materials.