Windows A does not overlap Windows B when done loading

Hi, i have another question. Let me state a scenario for a clearer picture. I am running a window A, and B at the same time, both of them are running data. Since i input the data in windows A, i will let it run and proceed with the data on windows B. But when A has done running before i can complete windows B, it will pop up and overlap windows B that hinder my inputs. Is there a way to allow them not to pop up and remind me that it has completed the process? For instance, blinking behind windows B will do.