Questions like these belong in Quick Questions, which is what this has been merged to, incase anyone has further input.
Not really sure how many masterballs you have, since it sounds like you've got many, but my best suggestion is to use masterballs on roamers like Thundurus, cause they're time consuming and annoying.
oops i mean i've used ultra balls on most of my pokemon like thundurus and zekrom
whats the best pokemon to use the masterball with? or shoulud i just keep it? seeing i've used a ultraball with thundurus