Upon buying your bubbler, you should be able to notice a part called a stem.
The general rule to this is that the stem should be submerged in water.
You can eyeball this as long as the water at least covers up ¾ of the stem.
The reason for the submerged stem is that the smoke will travel through it, producing a smoother hit.
Although this is the general rule, double-check the bubbler that you own as other bubblers have longer stems in them, which then changes the idea of how much water should be in it.