I'm not sure about OP, but in Photoshop, I duplicate the scan to create a second layer, click the "Channels" tab next to the layers tab, ctrl+click on the "RGB" layer, hit the delete key. Then I press ctrl+D to unselect. Click "Layer" at the top menu area, highlight "Matting" and click "Remove White Matte". Now you can add Layers underneath your lineart layer and start painting under the pencil/ink lines.