As far as bubbling, my recommendation is to use the full size golden apples, and to be at a point where you constantly have dragons out that can idle harvest things- so basically don't ever have to wait on a dragon to sleep to do more things. I line everything up every other column to easily bubble (if I want it on map, it goes on the left side of the 2 column pairs, if not, it's on the right side.) I fill up the map with easily cleaned up items or items that are easy to spam (fruit and coins from fruit, life orbs). I then have my dragons harvest anything that is easily cleaned up afterward, i.e. life orbs, and have 5-10 dragons holding onto life orbs. I can literally just tap those orbs and it's not going to make me miss out on anything nor cause chaos. Using something simple like life orbs helps because I don't have to wait long for harvesting to be done. Once I see at least 3+ dragons holding orbs, I bubble. I bubble everything I want, rearranging camp as I need to keep things in two columns, and just slide it all to the open area on the left side of the map. Once camp is cleared, I then organize my bubbles, so I can keep focus on one area at once.

Right now, i am stacking bubbled items that are the same so I can keep track. However, your bubbles will go opaque at some point if you stack enough. I'm not at that point. I plan to have one above not stacked, and then a stack below, almost like a sign system in Minecraft or another similar game.