The short answer is to set up an iPad exactly the way that you want it. Put the apps in the right folders and tweak the settings to your heart’s content. Once you have everything the way you want it, create a backup of that iPad using the Apple Configurator and use it to restore the rest of your fleet.
I’m not sure how well this will work for the incremental rollout of apps, but it should get you off the ground while you investigate further.
When we did our first rollout a year ago, the Apple Configurator did not exist. I used it in small batches, but this year is my first major rollout using the tool. I’ll be sure to keep you posted with any and all tricks and tips I pick up along the way!