You have to "smelt" the netherwart (with some coal for fuel) in an Alchemical Furnace with two Arcane Alembics stacked on top of it (you can stack up to 5 Alembics if necessary). Since Nether Wart only contains two aspects (Praecantatio and Herba), you only need two Alembics. Start by putting the Netherwart in with the coal, then apply a Label to each Alembic (so they won't switch places all the time). Place one Essentia Tubing on each Alembic and attach a glass jar to the end of the tubing. You will need one glass jar for the Praecantatio and I prefer to use a Void Glass Jar for the Herba (since I never use Herba). When the jars begin to fill up, put a label on those as well.
Now you can make Glass Phials and right click the Praecantatio Glass Jar to fill the Phial. It will now contain "8" of the Prae essence, so if Thamium reqires 4 essence, then each Phial will make 2 Thaumium ingots. So just throw the Phial into the Crucible, and then throw 2 iron ingots in, one after the other. You should receive 2 Thaumium ingots! Hope that help you understand the process. Later on, you can automate the Crucible process so you don't have keep using Phials and doing it by hand (I think it's called the Thaumatorium, just keep researching and you'll get to it).
Basically, you will want to make Glass Jars for all of the common Essences (such as Ignis, Terra, Ordo, Praecantatio, etc.) and make Void Glass Jars for all the "oddball" Essences (such as Herba when you are breaking down some Nether Wart). Make a place to store all your Glass Jars, later on you can use Golems to keep all your jars filled, etc.