Using pipes to try to get your Essentia to the right place is a hassle, and mastering them correctly can be a nightmare. Thankfully, there is an easier way to move Essentia from one place to another without needing to build a complex piping system.
In order to unlock Advanced Essentia Transport, you will need to quickly dive into the Arcane Infusion Tab (on the left when you open your Thaumonomicon).
Clicking on Basic Infusion will unlock this for you. There is no need to do any research yet.
Going back to the main page of Arcane Infusion will give you two more stages you can dig into. Currently, you only need to unlock infusion:
You need to scan a few things, do a little research and have the following in your inventory:
Once you have these, complete this research. The next stage will require you craft a Runic Matrix. The materials are simple and you should be able to create this without any issues.
Craft the Runic Matrix and jump straight back into the Alchemy Tab. This guide covers Infusion later on. Keep the Runic Matrix in a chest as you will need this later (also scan it).
Under the Advanced Essentia Transport stage, you need to do a little bit of scanning, but if you have been scanning as you go then you should be able to complete this straight away.
You should be able to craft two new (and very important) items:
The Emptying Essentia Transfuser goes on the Thaumatorium, and the Filling Essentia Transfuser goes on the Alembic:
This is far easier than having lots of pipes around and it looks great too.
If you place your Thaumatorium near the Essentia storage system that was explained earlier in the guide and you place a Emptying Essentia Transfuser on the Thaumatorium you can craft items with no need for pipes: