So far you have used the Crucible to make various items, but there is a simpler way that has little to no risk of letting flux into the air. By automating the Crucible, you will no longer have to throw materials in by hand.
Researching Alchemical Automation will enable you to craft the Thaumatorium. This can be crafted by putting two Alchemical Constructs on top of your Crucible and right clicking it with Salis Mundus in hand:
The Thaumatorium makes creating things such as Thaumium and Alumentum very easy, by simply hooking up jars, pipes and a chest to it. The Thaumatorium will automatically pull out the requires Essentia from any Jars that are hooked up to it. There is no need to worry about pressure or any other valves/pipes. Ensure that there is a flame below it (just like the Crucible).
All you need to do for the Thaumatorium to work is to make sure that it's constantly full of catalysts and has enough Essentia and that it’s creating the right thing. Once you tell the Thaumatorium what you would like it to make, it will remember the item and keep crafting that item until it has run out of resources.
When right clicking the Thaumatorium, you need to insert the catalyst for whatever you are crafting (in this example, I am crafting Thaumium, so my catalyst is an iron ingot). You can then select the item you wish to craft and it will tell you what it requires.
All you have to do now is click the desired item, and it will start looking for the required essentia.
It will also display what item it is crafting on to top of the furnace. Adding a chest to the front will store the output:
Not adding the chest will force the Thaumatorium to spit them out. This could cause lag if there is a big build up of items.
You can add as many Jars as you want, just make sure they are not all empty.