Now that the basic layout is there it is time to start inking in the final lines.

First reduce the opacity of the sketch so that you can use it as a guide, but you can tell what is being drawn now and what is the sketch.

Create a new layer and name it appropriately. I called mine DeckLines. This will hold the ink lines for one of the large objects in the image - in this case the ship's deck.

Click image for larger version. 

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Now before you go any further, it is quite likely that you want to refine your sketch. In this case, create a new layer called sketch2 over the desaturated sketch layer and begin a more careful sketch. Here's the progression of sketches I used to get to my final boat layout for this image:

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Each one was drawn on a new layer above the older one which was desaturated as shown. Once you have got a newer sketch then you can ditch the older one. The best way is just to hide the layer by clicking the eye that is beside it in the layers palette. You don't know when it will be worth going back to one of these older sketches.