First step is to find the Vis ( the "s" is silient) Crystals. you need at least 3 types you should get a note that you should sleep. sleep in a bed and you'll get a written book. read it and then take 3 different crystals, a flint, red stone dust, and a bowl to get Salis Mundus. Then rclick that on a bookshelf(Research enhancer) . NOTE: you can make salis mundus without sleeping, but if you don't sleep you can't use it on the bookshelf. Open up your Thaumonicon. read "the first steps" this will begin your research. you'll know at the book of the first page is a goal you need to complete. the icon on the left (of a hammer) means it's a crafting goal. you must craft this item. Obtaining it isn't enough you have to actually make it. as it says in the book, make more salis mundus and use it on a crafting table. NOTE: it has to be a crafting table, not a crafting station. reopen your Thaumonicon and go back to "First Steps" and click complete. Now you will see two goals. The top one (the scroll) means you need research in that field. the second one(hammer again) is a crafting goal. Note that the recipes are on tabs on the right. You'll see in the Thaumometer that there are 6 crystals on the bottom as well as the number 20 with a wand behind it. The crystals show how many of each Vis crystals you need and the wand number shows how much Vis you need in the area. Make your Thaumometer and start scanning. NOTE: you can now scan chest and everything in the chest by Shift Right Clicking them. no more throwing items on the ground to scan them. items you haven't scanned will have blue sparks around it, but will take time to update once you do scan them. after scanning just a few items I had enough levels in Fundamentals to complete the quest.
In your Thaumonicon Fundamentals page you will note two other sections Types of knowledge and Theorycrafting. Types of knowledge shows your levels in types of research, this will be important later. Theorycrafting is how you can progress your knowledge levels. make a table and a scribing tool, and lots and lots of paper. Note having certain objects around can aid in your research.
Now you can start "Discovering Alchemy" if you don't have enough knowledge levels start doing Theorycraft or scan more items. I had enough so I clicked complete. Now we have to make a Crucible (Research enhancer) get a cauldron and some Salis Mundus. You need heat under it. I recommend Lava and to put an infinate water source nearby as you will need to refill it often. Complete the quest.
now to make Nitor. 1 coal and 2 torches with a glowstone will make 1 nitor with a little left over. This unlocks the Alchemy tab and lets you read Basic Alchemy. It also unlocks Auromancy and Artifice & infusion.
Automancy ask for "things to be discoveried" you must find something that fits this. in this section it asks" Visit the lowest depths of the world"(get below y 10) and "Visit the highest peaks you can find"( get over Y100). You also need an Epiphany. once you have those click complete. Here we will learn that wands are no more and instead are gloves. be very very quiet as you hunt those bunny wabbits. make your resonator and gauntlet and complete the quest. This will unlock the tab.