You determine which creature to put counters on as the spell or ability that instructs you to bolster resolves.

Bolster itself doesn’t target any creature, though some spells and abilities that bolster may have other effects that target creatures. For example, you could put counters on a creature with protection from white with Abzan Skycaptain’s bolster ability.

Each Dragon you attack with will cause Dromoka’s triggered ability to trigger. For each instance of the ability, you’ll determine which creature to put +1/+1 counters on as it resolves. Specifically, the creature you control with the lowest toughness as the first such ability resolves may not have the lowest toughness as the second such ability resolves.