Ok XDD I think your problem is in the settings. When you click under the magic want tool It'll say "Detection mode," which I don't really know a whole lot about other than I always have it on "Color Difference," not either of the transparencies, and the color difference is 0. Under that, which I think is probably your problem, it says "Target." You want to check "Working layer," because then the magic wand only reads what's in that layer, the lineart layer. If it's in "Selection source," and you don't have anything selected in the first place and you don't have a layer marked as your selection source, then it'll just highlight the entire image. If you have "All Image," then it will select from the entire image, if there's a change in color in any of the layers. Also make sure Anti-Aliasing is checked--that makes the colors fade to transparency so they don't stair-step and leave as many white holes.

Here's a coloring trick it took me awhile to figure out :3 but it helps a lot. Instead of using the magic wand to select the inside of the lineart, select the outside. Then go to the "Selection" on the very top right, click "Increment 1" a few times (Usually only once or twice, depending on your resolution and canvas size) so it selects a little bit of the lineart as well. Then go to "Selection" again and click invert, and it'll invert the selection so you're now selecting the inside and a little bit of the lineart. Then when you color on a layer underneath, it won't leave white holes around the edges, other than certain places where your lines change direction sharply.

Hope some of this helped! Oh, and when you fill with the bucket after selecting with the magic wand, make sure under "Target" for the bucket you have "Selection source," highlighted. Because then it'll do the whole selection and not stop awkwardly a pixel or two from the lines after you spend the time incrementing.

NOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO

OH MY GOSH THANK YOU TY!! XDD I think I'm already watching you :3