>>Choose what block and height of the layer you want and click the "Add layer" button (You can also click the "Advance Settings" and type the Block ID, Block Data and the height by yourself) >>Set Biome/Structures >>Click "Generate". A code will be generated and you can copy and paste to the Minecraft Superflat Costomization Preset code box =]
I made it easier to understand. Also, bedrock is now automatically added by default, and can be removed. The bedrock layer ID is 1x7. UNOFFICIAL MINECRAFT TOOL For use with later versions of Minecraft 1.7.x. The versions of Minecraft that this tool is compatible with has remained unchanged. Current version: 2.6.0 I did not create version 2.6 and am only putting it up here for users of newer Minecraft (1.8-1.12). The link is http://www.minecraft101.net/superflat/