Buildbox uses the screen size of iPhone 5, 640x1136. So set assets to the according size for that screen (a little bigger would be better) and Buildbox will scale that into bigger screens or smaller screens. If you drop very big assets into buildbox and scale them down from there, then when testing your game you'll notice they are kind of sharp, and if you do the other way around and you scale them up, they will become very blurry.
This is how you end up with 89 atlases (search it) My suggestion is to create your assets... Bring them into buildbox... Scale them to where you like.... Note the percent of the scale... Delete that object and delete it from your atlas... Resize a copy of the original the percentage that you noted... This will keep your atlases low in number and your game file size small