After I'm done with rough sketching I may go for a clean sketch phase. It's not always necessary since you could paint from roughs too.
With roughs as a base I drew a relatively clean outline in Painter or SAI using new layer and pen tools. SAI is good for long fluent lines while Painter is perfect for crosshatching but that's just for me. Sometimes lineart doesn't look right so I've to redraw it 2 or 3 times.
I keep details (belts, buttons etc.) & cloth in separate layer so some further design changes/revisions wouldn't affect the figure.
I also played with a tattoo designs in an additional layers.