Hi,
Without knowing the current status of the system I cant comment on exact areas which will have an impact, but I can give you some hints.
Controlling module integrate with all the other modules. If your planning to change the master data such as cost centers, profit centers then you have to consider the MM, PP, SD, master data assignments (materiel masters..,work centers etc), automatic assignments such as OKB9 settings etc. further if FI_AA module is implemented then asset masters may also need to be changed (cost center assignments for depreciation)
If your changing Product costing related configurations then it will have a major impact to PP module and I suggest you to consult a PP consult for those changes.
Actually depending to the components you activate in Co, you need to check the impact to all the other modules. If COPA is activating then its another areas where it has a direct integration with SD & PP, depending of then level of profitability you need to report.
controlling module is a internal management accounting tool, there will be changes to your internal business processes as well hence you need to have a detail plan for each area & proper cutover strategy.
Regards
GayaniP