Maker - Alchemy Skill FAQ and Walkthrough

^ that.

Looking at the picture though, there seem to be 4 possible slots for jewels (1 is available, 3 are crossed out). Maybe it goes 1, 2, 4, or maybe there's a level 4 in the future?

I think it's just a place holder for there being 4 in the future. The skill's max for the moment is 3. Since you can only use 1 diamond, the most useful thing to do would be 1 high grade diamond and 1 high grade Stat crystal (STR/DEX/LUK). With that it doesn't really matter what you put on your 3rd slot. I guess you could put your secondary stat, but since most people only use the secondary stat to equip a weapon, it's not gonna do you much good.