The way you create your comics matters less than the quality of the comic. It's true that coloured comics tend to grab more attention than comics in black and white, but you can colour comics traditionally too, so it's not a matter of medium there either.
I do my comic 100% digitally (except for thumbnails on paper), but I've done comics and illustrated stories entirely traditionally too. Both methods work, they're just different ways of creating.
As for layers.... Ask any digital artist - we are CONSTANTLY drawing on the wrong layer and having to undo and start stuff over! >.< I've started locking my lineart layers to prevent myself from accidentally colouring on them, and the other way around. I also try to cut down on the number of layers I use, because if I don't keep track, I end up with files with 40+ layers. I keep lineart on one or two layers (1 for characters, one for backgrounds), flat colours on two layers - one for the backgrounds, one for the characters - then I do shading on one layer, and extra lighting effects on one layer.
