Alchemy is a bit of a chore when trying to put in the exact amount of a certain Essentia, and can cause flux. To avoid this you can smelt Essentia. To complete this section you will need to have all six basic crystals in your inventory.
This will use all six crystals. The next part will require compound Vis Crystals.
These are crystals made up of more than one Essentia. A simple way to get all of these is by adding items to the Crucible and then Slivering the aspects out:
It doesn't hurt to have extras of these as you might use them for crafting or research. Once you have these in your inventory you should be able to complete the section.
Next, you will need to research more for Alchemy, and you will also need to make a Essentia Smeltery. Check with your mod pack to see how Brass Plates are made as these differ with each mod pack:
When researching Alchemy, you can get a bonus with your Crucible. Some of these notes might need Vis Crystals, so keep a stockpile.
Once you have completed the section you will be able to craft the Arcane Alembic, Warded Jars, Void Jars, Blank Labels and Brass Lid Braces.
You will need to wear Goggles of Revealing for this next part.
So how does all this tie together? Well, the Smeltery will break down items directly into the Essentia it is made of. Use coal or any other fuel to power it (Alumentum works best) and store them in its inventory. When you put a Alembic on top of the Furnace it will extract one type of the Essentia. The downside to the Smeltery is that it has a 25% chance of generating Flux as a byproduct. It also is only about 80% efficient (losing some Essentia in the process). If you put sandstone into the furnace and look at the Alembic, you will see it start to fill up with Terra. you will also see some Flux being generated:
You can then right click the Alembic with a Warded Jar and it will put the essentia into the Jar. Each Jar can only hold 1 type of Essentia, and can hold up to 250 of it. Once you have removed the Terra, the Alembic will fill up with Perditio. You can also remove this by right-clicking with a new Warded Jar.
You have the option of creating labels, but 37 labels takes a lot of slime. Alternatively, you can simply use Goggles of Revealing. However they do have the added benefit of retaining the label after they are emptied, and will only allow the Essentia that matches the label.. The Jars will retain their contents when broken (with or without labels):
You can extract the Essentia from the Jars (and the Alembic) with a Phial, but these will only hold 10 of each Essentia (can also be used to put Essentia into Jars by sneak-right-clicking)
This can be an easy way to add Essentia to the Crucible.
You can also use multiple Alembics (up to five). Once one is full, the next one will fill up (or more likely, if an item contains multiple aspects, one Alembic will start filling with one aspect and the next will start filling with another aspect, and so on). Filling priority is from the Alembic touching the Smeltery and up.
Void Jars can be used to delete the excess Essentia (use a label to only void the type indicated).
This is not the most efficient way to collect Essentia from items, but you can make this process a little easier with the help of Tubes.