Traditional manga artist usually ink right on top of their pencil originals; once the pencil sketching is complete, they sweep the dust and eraser bits away with a feather brush, then use a variety of inking nibs and brushes (mainly nibs) and apply ink lines right on the sketch. After the ink is dry, they erase the pencil lines. Then, they apply the screen tones if they see fit.
More recently, many artist prefer to print out their pencil sketches as blue art then ink on top of that. This way, they preserve their original pencil sketch.
I have not met many people inking digitally, but it is possible. The best tool is the scratch pen tool in Painter. In Photoshop, pick a brush that does not give you a grey trail; something crisp and clean.