So I want to color something in another layer but it goes through the black lines and I want it to not color anything that is black.

What do you mean by "it goes through the black lines" Can you show an example image please?

I want to select everything that is black and not go through it.

Try "Select by color tool" click on any color black in the layer. Now select "Select Invert" now paint.

Draw the line art in a transparent layer then color underneath on another layer.

Just move the layer with the red lines under the layer with the black ones. This can also be done before you paint since painting goes to the active layer, and not mandatorily to the top one, so it is possible to paint "under" something by selecting a layer under before painting.

It was my understanding the black lines and paint are on the same layer.

The crux of Gimp is to use separate layers whenever appropriate.