The alembic is a block that can be placed on any one of the four sides of a Crucible. Alembics will store the unused essentia left over so it is not released as flux. However, you are only able to store essentia of a single aspect in an Alembic at any given time. Up to four can be used to collect unused aspects. You can collect this with phials in groups of eight essentia, but only if there is already eight or more units of the aspect already collected. If you wish to dispose of it without collecting, with a wand, you can sneak and right-click the alembic to release the essentia currently inside it. Be warned, as doing so will increase the Flux in the local Aura, because you are releasing the aspects into the the Aura.
Here's a video that explains how Alembics work:
"You have taken your first steps towards understanding and managing Flux. Your research has led you to two practical applications: The Flux Filter and the Arcane alembic."
Alembics can be monitored by Tallow Golems. The Golem will take phials from the nearest marked chest and if there are at least eight essentia in the alembic, it will take the eight essentia and store them in the nearest marked Warded Jar.