Thanks for responding! I tried the cell-shading select tool, which worked to copy/paste on the canvas itself, but still wouldn't copy from a different canvas. The image I'm copying is actually a bit larger than the canvas I'm working on; it's a screentone jpeg saved off of Manga Studio. I was copying pieces of it and pasting them over my outline to tone a comic. I also tried copying and pasting into a selection, to make sure it wasn't pasting somwhere off the canvas, and used the "move" conrtol to drag the blank layer back and forth, but it stayed blank.
Well, do to it being a different program, post it in your scrapbook here on deviant art, i believe you do not have to use key words on those their just and option so it will be easy to post, make it big if you can, if your using google chrome right click and copy image, if IE right click and copy, paste it into Sai that way. if still no sorry D: