I am trying to figure out how to make the paint tool paint the entire closed area, and not leave a border against my brush stroke lines. Do I have to do my final drawing in pencil to avoid this issue? I posted a picture down below showing the problem.
You are using a bitmap brush and painting on the same layer? You should have better results drawing on the Line Art layer and filling with colour on the Colour Art. You would have to create colour art from line art. Check the docs for Creating Colour Art from Line Art: https://docs.toonboom.com/help/harmony-15/premium/paperless-animation/about-art-layer.html
But even with textured bitmap brushes it’s strange you’re getting that result. Is that a brush that you customised? It looks the same when you render the frame?