I am using SAI as an animation tool and therefore I will need to save the layers as separate images so that I can use a different animation program to put them together. Is there any way to do this?
If you want an accurate (rough or otherwise) animation, I would suggest to draw the first (frame), and turn the line work to a red, or a strong, semi-dark color. Lower the opacity.
Make another layer, then draw your next frame. Turn the line work into a lighter contrast color that pairs with the last; repeat the process, turning every other frame, say, (red, green, red, green, etc.)
To get the frames into another program, it is very tedious, the way I do it. Save every layer as it's own separate preferred image file (.png, .jpg, etc.), and open each into your preferred animation software. Select each frame, and copy each frame onto one alpha layer.
I recommend you turn them back to black (or your original color of choice,) because most animation softwares do the onion skin affect for you.