You can easily color in your line art by turning the bright parts of image transparent.

When scanning in an image, it will have an opaque background so if you try to color on the layer underneath it, it will look as if you aren’t painting at all.

To check if your line art is transparent or not, hide the paper layer. If a grid pattern appears where the bright parts were, it is transparent.

Left: Opaque - Right: Transparent

If the line art has an opaque background, you will need to make it transparent.

Select the imported line art layer, and select [Edit] menu > [Convert brightness to opacity]. This will convert the white parts to transparent, and you can then color in the line art from a layer below it.

Note: Images scanned directly into Clip Studio Paint, or imported via [File] menu > [Import] > [Image], will be created as Image material layers.

You cannot use
[Convert brightness to opacity] on Image material layers.

First convert the layer in a raster layer by selecting [Rasterize] from the [Layer] menu, then run [Convert brightness to opacity].