The answer to this question is totally up to the bride and groom and the age a temperament of the children involved. If the children are older and you want to capture many photos from the ceremony, with them in the photos. I suggest that they stand at the front with the bridal party.
Of course, sometimes this is not an option and they are simply too young. If that is the case, I suggest the groom gives them some sort of embrace/high five, so the photographer can capture this. The flower girl or paige boy will then sit down with their parents.