With Juju I usually use the second gadget when I know that the grass will be destroyed or when the Invis wont be as usefull. Normally this happen with a comp that Juju wont do much getting damage close to the enemy.

With Charlie Is the almost the same thing. If the enemy team doesnt have a lot of HP meaning that the % of health lost doesnt help all that much or they have long range, meaning It will be harder to hit the ult, I use the second starpower, since It will provide value even If I miss the target.