I did 3 split stays last year. I'll probably never stop with them, because I want to experience different resorts but I love to end up at my favorite, Y&BC.
I always have my young son with me, and the most recent trip involved 5 adults and 3 kids under age 6, and it was still fine. Definitely make the "nicer" resort--or the one you're just more excited about--the second resort.
I always have a car, which helps. I have let Disney move my luggage but I prefer to do it myself, because it can take them awhile. When I let them do the moving, I carry a change of clothes.
I think the key to a seamless split is staying super organized and mindful that you're leaving Resort 1. If you prepare for the split at home before you leave, it's easy and doesn't kill any WDW time. As previous posters mentioned, packing two separate bags simplifies things, or you can use packing cubes to organize two trips within one suitcase. I don't really unpack at Resort 1. I have a cool toiletry case that hangs on a towel bar and has all kinds of zippered pockets, meaning I put things back as soon as I use them. I pack an expandable duffel in my luggage for souvenirs and dirty laundry. I don't lose any time packing for Resort 2 because I've been doing it as I go, and the extra bag means I don't have to play Tetris with my luggage for the split stay or for when I finally leave to go home.
Normally moving day is a "day off" -- we stay at Resort 1 swimming or relaxing right up until check out at 11 a.m. I make a 12-ish lunch ADR somewhere, usually at another resort. By the time we load the car, eat lunch, explore that resort, and get back in the car to go to Resort 2, it's pretty close to 3 pm check-in time. We don't feel like we're room-less for too long, if at all, which I think is important with little kids.