How to avoid confusions, during integration process? If in case, both organizations come from different cultural backgrounds, then how to avoid cultural clashes and also how to avoid mis understandings which may arise due to different protocols and way of thinking etc.
Setting the organisational goals and objectives from the start will help alignment. What is the end game and how do we work together to get there? Not everyone will get along but as long as leadership is aligned. Perhaps given the different cultural backgrounds it needs to be slowed down a bit and also some cross-functional team building?
Agree with the above comment, best way is to set up a common goal where the focus is on how to achieve it together. This should mean that the system, functions and processes that best help to meet the organizational goals will naturally fall into place. Often we find that the cultural differences actually become strengths because there are different perspectives in play to aid in problem solving.