If you prefer to draw your art using pencil/pen and paper first... scan in the art... crop to the correct ratio if necessary then reduce the image size to your pixel art resolution. e.g. 256x80.
Then in your image editor, push the contrast up to maximum... this will get rid of the grey and convert everything to either black or white. Then adjust the brightness setting to get you the desired line thickness.
Once you've done this you should have a black and white pixel art image that can be coloured. Make sure you turn off anti-alias when you use the fill tool to add colour.