The best way is to balance characters between each other (which is wise anyway even in 1 splat as options are not always well balanced), but the splat themselves... good luck with the headache.

Although be mindful of some mechanics that can make the mix unpractical (Vampire sleeping at night, Changeling Mist, Werewolves Delirium etc)

Mixing supernatural templates on one character doesn't really work, although (I believe) anyone (but Vampires) can be a ghoul though there are secondary effects. Alternatively, Vampire have theKiasyd/Maeghar for Changeling, the Tremere are...