We have done two split-stays and will be doing it again in June. Now, I can't imagine spending more than 5 days at one resort. It's like getting two vacations in one! I did learn, though, that we need at least 3 days at each resort to get the full flavor and experience of the resort. Anything shorter than that makes me feel like I don't even have time to unpack my suitcase.
On one transfer, we transferred our own bags since we had a rental car. The second time, my husband wasn't feeling well so we just called bell services and they took our luggage and transferred it. I'm not sure I would just leave my bags in my room, though. I wouldn't feel comfortable with that. I would prefer that someone pick them up before I leave the first hotel.
Both times, we went straight to the second hotel in the morning (8:30 am or so) and checked in, knowing that our room wouldn't be ready. I figured that way we got a better room selection than those people checking in at 3:00. Then we were off to the parks and when we came back for an afternoon rest, we called for our bags. It was very easy.
Also, remember that if you have any medications or special food items that you will need, to keep those with you. We had antibiotics and prescription cough medicine and we had to be sure to hand carry those in case our luggage would have been delayed.