Ok. ^^ I can't seem to find the tutorial I originally learned how to do it from, so I'll just say it here.
Open a new page in Manga Studio.
Import one of the new screentone's you want to add to Manga studio by:
File -> Import -> Image File
Change the image to fit inside the page.
If there happens to be any changes you want to make to it before saving it as a screentone, this is when you do it.
Now go to:
Edit -> Register Pattern -> Tone Material...
At the top of the new window, name the tone whatever you want it to be called.
Double click on the "User" folder and make a new folder and name it "Water" or whatever you want... I just do this to keep my screentone's organized.
Make sure the "Water" folder (or w/e you called it) is clicked and highlighted and press "Ok".
It should be registered as a screentone now for you to use.
When browsing your Tone window, go to the top and instead of clicking on Default click on User. It'll be there.
*Note: I use Manga Studio Debut 4... so there may be some differences.
I hope this helped you!