The unified inbox lists the contents of all folders that have the Unify setting enabled. By default that's all inboxes of all accounts. To change this:
1. Select the account you want to exclude in the side drawer 2. Tap Manage folders in the side drawer 3. Select the inbox from the list in the Manage folders screen 4. Uncheck Unify
(Even non-inbox folders can be included in the unified inbox by checking the Unify setting in their folder settings screen)