It really depends on how you structure it.
What my team kids do (both boys and girls) is include some conditioning (endo rolls, press handstands, limbers, etc) in their warm-up. My girls (more due to how our gym's schedules are structured than anything else) have a flex/conditioning rotation at some point during each practice. Sometimes it's at the beginning, sometimes at the end, sometimes in the middle. In addition, I try to set up some light conditioning as a station in our rotations.
My boys do a bit more conditioning and I'm a bit more rigid in how it's organized. Like the girls, the boys do endo rolls, presses, and limbers during their warm-ups, and have some manner of conditioning as a station in almost every rotation. But as for a dedicated flex/conditioning rotation, I always do that at the end. This allows me to give them higher intensity conditioning without worrying about tiring them out for subsequent rotations; I do my best to have them completely worn out by the end of their conditioning rotation, since they'll just be heading home afterwards anyway.
So it depends on the nature and the intensity of the conditioning. I tend to prefer conditioning at the end of a workout when possible, simply because they don't have to save their energy at that point, but this is more a matter of convenience than one of necessity.
