In a nutshell, it's a frustrating experience. Vallejo recommends rolling the bottle in your hands. Mig Ammo sells steel ball bearings to insert into these bottles to improve getting the pigment into suspension. This method is fine for Model Air, but not so much for Model Color.
The Badger mixer for all other paints works well to fully mix and avoid air in the suspension. Unfortunately, the mixer is too broad to fit through the neck of the 17ml bottles.
One guy on YouTube shared his method of inserting the bottle into his electric drill which seems overkill.
What method have you found that ensures thoroughly mixed paints in the 17ml bottles?