Say you draw your lineart and save it as a B+W image, or you draw your lineart on a white background layer. Either way, at one time it was just a sketch, but now you want to go back and color it, and do some stuff with tinting, etc--so you want it on a transparent layer again.
This is how you do.
This is a relatively straightforward process once you understand how masks work. Though I wrote this for Photoshop, you can do the same thing in Sai (if hotkeys are different, understanding the process will allow you to figure it out for yourself).
A mask converts the VALUE of a pixel into an amount of opacity (with 0 0 0 black = 0% opacity and 255 255 255 white = 100% opacity). As a result, they’re always grayscaled.
Essentially, the layer is totally filled with black. The mask makes it so anything that contains white (which, once inverted, is your lineart) will be the only thing that actually shows up on the canvas. Applying the mask simply erases anything that doesn’t show up, giving you the original lineart.
Naturally another option is to set your lineart layer to ‘multiply’, but alpha lineart is still pretty important for other applications.