Thanks so much for reaching out! Those are great questions. While it does come down to personal preference, I would personally recommend option 2. I think that the ability to navigate through each workshop individually is the most flexible and stable option for what you're trying to do! Having all of the cues in one script could work, however, given there are so many videos and things you'd like to use, the less in ONE script the better, as videos are very large in size so they start to weigh down a script if there are so many of them at once.
If you have any more questions about this, let me know, I'll be happy to help!
Thanks and God bless!
-Ben Wagner, MediaShout Support and Sales