Just as long as you don't lose any of your astral uptime, dot away. Multiple proc sources help a lot, but it's not really a yes/no answer or an X number of dots on X mobs answer. Just make sure not to overlap thunder on a single target if there are multiple targets up. When you get a proc, spread the love to another target, and so on. Just fit as many thunders in as you can without messing up your fire rotation. More of a priority system than any specific rotation.
To answer your specific question, I usually multi-dot on the children, but unless I get a flood of procs somewhere it'll only end up on 2 or 3 at a time. For the second set I'm on LB, so I generally go into UI, put up 1 thunder while the tanks get into position, LB, and since I start my rotation from full mp at that point I can drop another quick thunder on someone else.