Ew.... Never use the bucket tool. I hate that tool, everything gets all pixelated and stuff when you fill things in. I prefer colouring things by hand. If you ever do use that horrid thing, use the the magic wand (correct me if there's no such thing, I haven't used SAI in a while) to select the inside of the lineart.

Don't do everything on one la
yer, organise your layers. Make sure the lineart la
yer is on top, make a new base colour la
yer and then a shading la
yer on top of your base colour la
yer that's set on 'multiply'.

I first tried layering when I got Paint.net and gave up on it (which I know was a stupid thing to do).  Then I got GIMP and didn't even attempt layers then.  But when I got SAI, I wanted to try again.  I'll try coloring by hand. =3

EDIT: Ah, got it.  Thanks so much. ^_^

Sorry but, I don't think you understand the concept of layers.They're really simple. If you don't use them in digital art, you are most likely going to be spending hours undoing mistakes. Y'see, if you draw on a la
yer that is underneath another la
yer, the junk on the bottom la
yer will appear underneath the top la
yer. It's simple.

Yeah, I know I don't understand it well. >.< I'm trying though.  I used the three la
yer method like you said to make a last minute contest entry for Geo's contest....I got dragged off the computer before I could fully finish shading and fixing things though. ;P I know it's not the best, but eh.  I'm only a child. XD