We use prioritisation meetings to set the priorities for the teams to deliver on projects, I do understand that the BAU activities have an impact, but we try to manage that by adjusting their utilisation times i.e. 60% BAU and 40% integration. If the integration activities are to much for the BAU team we use specialist contractors/consultants on outcomes based contracts to supplement and support the integration activities. Building these costs into the plan early on makes it easier to do when it comes to doing integration tasks. If you can it should be added into your intitial high-level costs of doing the deal as part of the Due diligence process.