How does creating custom skills in Fate core work? Can you just say "I want this skill" and get away with it or is there some sort of preset rules such as designing stunts and such for the skill before adding it to the game? To be specific, I want to create a skill called Magical Engineering as my character will not be knowledgeable about lore or be able to craft most of the things.
The Fate SRD deals with creating new skills in its System Toolkit section. It goes into considerable detail including modifying the basic list by addition or removal of skills and grouping skills into "modes" or "professions".
You might want to define a "restricted access" skill as an extra.
Alternately, if your entire vision for this skill is "Lore, but it can't do as much", you might want to consider one of the following approaches:
Take Lore at a low rating, or perhaps don't at all, depending, and a Stunt that gives you +2 to use Lore for things that fall under the auspices of Magical Engineering. It should probably be narrow enough that it's reasonable for a Stunt to boost it under those circumstances.
Take Lore at the rating you want Magical Engineering to have, and also the Aspect I'm An Engineer; I Solve Practical Problems. Whenever you're in a situation where it would be useful to know something about magic or history, darn the luck if that ain't one of those conundrums of philosophy.