Inquisitor's Flail doesn't let you assign damage any differently, it is merely a replacement effect for how damage is dealt. So essentially, you have a 5/2 trampling Runeclaw Bear up against a regular 2/2 Runeclaw Bear. You must assign lethal damage to the blocking Runeclaw before you can assign any damage to the defending player, so you can only assign a maximum of 3 to the defending player. When damage is dealt, Inquisitor's Flail doubles everything, resulting in 4 being dealt to each Runeclaw Bear, and 6 being dealt to the defending player.