Sorry, I'm not much help on your question but I had to turn around and ask you one! Without any experience in doing that, I might collect your luggage yourself just so you know you'll have access to it when you need it. If you have them transfer, it's gone until they decide to bring it (and occasionally things do happen...)
My question to you - how on earth did you get reservations for that weekend at Epcot resorts???

Do they hold rooms for the convention rate and Disney Institute you mentioned? I was looking recently for 11/13-11/15, and initially there were no rooms anywhere on disney property! I called CRO and had a disney TA look as well. My TA said he hadn't seen that happen, where you couldn't get any room at any price anywhere. Since then some have intermittently opened up, I got the CR initially and then found a Poly studio so we're just a monorail ride from Epcot. My top choice would be any Epcot resort, and nothing at all has ever popped up when I check, Given that it's the last weekend of F&W I'm not surprised it's booked, but then I read your post. I'm jealous, and curious how you did it? I am happy with the Poly, but I've never stayed at an Epcot resort and thought this would be a good time to try it. Spontaneous trips during F&W weekends make being picky about resorts hard. I remember when this was the slow time.