Note both Manga Studio 5 and Clip Studio paint are the same program. Some of the options may have different names between the programs, but the features are the same. Smith Micro (I believe) is slowly phasing out Manga Studio as a name and going forward will be sticking with Clip Studio on all future releases. So these instructions should work for either program.
In this video I show you how to use some of the special options in manga studio 5/clip studio paint to make your flats layer for coloring more quickly. A flat is a layer of different colors under your art that is used primarily for selection of large blocks of a piece (like a face or a hand). So that when you have a bunch of other layers but want to get back to just that hand, you can do it using the flats layer. I use a couple of tools in this video including area scaling, reference layers, and a brush feature called “anti-overflow” to make this a more painless process.
Special thanks to Dan Hale for the lineart that I used in this video. Here’s his website and the comic this page was from: