Open up your program and then select Window < Beginner's Assistant. With that, the drawing options/layers are set into their own tabs, and tones has its own.
Select the tones tab, and it will have all the ones available, and then ones sorted in sections. It may take time for all of them to load (no matter which section you choose), there are quite a few of them.
You drag and drop tones to use them. You can either fill the whole page with just a single drag and drop, or you can use the rectangle/lasso/polyline to be more specific, and then drag/drop the tone into the dotted lines. The tones create their own layer so you can erase as much as you want.
As a quick tip: When you're using tones in Manga Studio (ANY version), never ever never overlap the tones. It's worse than crossing the streams in Ghostbusters!
The reasons why won't seem important on your screen; Overlapping the tones won't appear to cause any problems.
. . .Until you print.
What happens is, to your printer, the tones are a pattern of dots. When overlapped, the printer prints both these patterns, one over the other. The result? A weird, square pattern appearing within the tones itself--called moire. It's not technically an error--so there's nothing wrong with your printer--and the only way to fix it?
To edit every single pages with overlapping tones and delete the overlap! If this has happened to you, my tip is to go to the layer with the least amount of tone that overlaps a larger area. Select the smaller bit of tone, switch to the layer with the tone it overlaps on, and delete the selected space 8D