Apothecary Guide

In order to craft a potion with apothecary, you need a minimum of 3 items: a container, a main ingredient, and a stabilizing ingredient. Basic containers, and level 1 sub-ingredients can be purchased at merchants (not quartermasters) and craft merchants. As you gain levels and move up to different tiers, a more advanced container can be purchased from the merchant.

Here's a breakdown of the process of making potions:

1. Place the container in the container slot
2. Pick a main ingredient from your inventory and put it into the main ingredient slot
3. Put a stabilizing agent, usually cloudy water to start, in the first slot, and check the bar on the right labeled "Potion Stability" above. If the arrow is at the bottom, crafting the ingredient will cause the vial to shatter and the synth will fail. If it's halfway up then you have a good chance of getting a potion but it will be volatile. Volatile potions have a chance of doing the opposite of what they say they'll do (Example: you lose 25 action points instead of gain them).
4. Keep stuffing stabilizing agents in until the potion is either halfway or at the top (I usually go for the top for potions that I want)
5. If you have extra spaces, you can put a sub-ingredient in. Sub-ingredients fall into 2 categories: Makes more potions and Increases Potion Potency. Also listed under sub-ingredients are other stabilizers not available from the vendor. These stabilizers are generally more potent and can reduce the number of waters you need so that you can afford to use sub-ingredients in your synth.
6. When you've got the mix that you want, hit "Brew", then enjoy the fruits of your labor!

You can read even more about apothecary here.