Popup or email is fine, as long as the job isn't ran if already ran for the day, and provided the popup doesn't continue the job.
The jobs themselves are basic. Once a few processes outside VisualCron are ready, we call the VC job with tasks that execute programs, FTP program output, then write results to a file. So we need something at the very beginning of each VC job that does the current/last run date check.