Have you created a Sync and/or Antisync profile? If you want your pumps sync'd then you need to do that and assign the sync profile to one of the pumps (in the sync profile it will define the other pump as the master). This way, pump 1 is the master and pump 2 follows along (sync) or does the exact opposite (antisync).
If you want them to be completely independent, then you have to assign profiles to each of them based on time of day, etc.