Hi!
My main recommendation...LAYERS. Fall is that delightful time when it's warm one hour, brisk another, so I'd pack clothes from short sleeved t-shirts along with complementary-colored long-sleeved ones and always have 2 kinds of jackets in the trunk. Having an extra pair of walking shoes for each of you is also a good idea in case the 1st pair gets muddy or wet.
As far as where to stay, I like the Westgate Smoky Mountain Resort and the Stony Brook Chalet.
Why don't you check out this trip (Fabulous Family Smoky Mountain Getaway) which is geared to families who are traveling to Gatlinburg with kids? It even gives the parents a little time to themselves (babysitting services). Plus, by clicking on the places & activities, you'll get lots of ideas for fun things to do there.
I've done a LOT of traveling with little ones (& even while they were still "on-board") and while it takes more planning to bring extra things for their needs, it's such a delight to see their wonderment over seeing new places & experiencing new things. Enjoy!