The Fate Rules has something to say about that:
Remember, you want a balancing act between obliterating the PCs and
letting them walk all over your opposition (unless it’s a mook horde,
in which case that’s pretty much what they’re there for). It’s
important to keep in mind not just the skill levels of the NPCs in
your scenes, but their number and importance.
Right-sizing the opposition is more of an art than a science, but here
are some strategies to help.
- Don’t outnumber the PCs unless your NPCs have comparatively lower skills.
- If they’re going to team up against one big opponent, make sure that opponent has a peak skill two levels higher than whatever the
best PC can bring in that conflict.
- Limit yourself to one main NPC per scene, unless it’s a big climactic conflict at the end of an arc. Remember, supporting
NPCs can have skills as high as you want.
- Most of the opposition the PCs encounter in a session should be nameless NPCs, with one or two supporting NPCs and main NPCs along
the way.
- Nameless and supporting NPCs means shorter conflicts because
they give up or lose sooner; main NPCs mean longer conflicts.
In the end it comes down to feeling, how does it feel? what kind of outcome are you looking for? And what are the players expecting?
Most importantly though, everything in the Fate world follows the Fate rules, so if there is a boss, you don't just arbitrarily decide what you will about his skills and stats, but you should create him using the same rules as you would create any character, here are some rules about creating main NPC's