The only reason one may not want to take Iodine later in the day is because it may interfere with sleep since some get a nice energy boost from it.
Aside from that take it when ever and how ever you like.
Vit C has a short half life, ideally you want multiple small doses spread throughout the day and in a perfect world take as much as you can without bowel issues.
The diarrhea that comes from vit C happens when it passes through the digestive system and reaches the colon. It causes a localized dehydration of surrounding colon tissue. If that happens it simply means the dose you took was too large to all be digested, simply reduce the dose.