Couver and Khloe travel with us all the time, and I find that having all of their necessities handy makes it easier when stopping. I pack their food, poop bags, water, leashes and treats in a bag in the back seat so I can get to them while we drive. I keep the rest of their things; clothes, extra food, treats, shampoo/conditioner etc in the trunk so that when we get to our destinaion, we can just lug them in with everything else.
I don't have any advice on bags as I usually just use their KB or a canvas bag that I have for them. I'm sure a diaper bag would be great to help organize her things and keep them accessible at the same time