Regardless of what medium you're using - pencils, paint, markers - you'll always get a much better result if you colour your image in layers. Start with a base coat then build on top of it until your image has depth and dimension.
I've coloured the octopus image from the new By The Seaside set with copic markers. As you can see, I began with a light base coat and then added layers of colour to create depth and shape. The light colours in the image are focused on the areas in the foreground, such as the top of his head and the front few tentacles, while the dark colours are added to the recessed areas to give depth.
Base coat with E51.
Second layer E53.
Leave a few areas with just the base coat showing.
Third layer E55.
Start to darken the recessed areas
and shape the tentacles.
Fourth layer E57.
Now you can see a distinct difference between
the lightest and the darkest areas.
Final layer E59.
These are the darkest places in the image.
First layer C5.
I've stippled cool greys around the image
to "ground" it on the page.
Second layer C3.
Colour over all the stippling you did previously,
then add more dots with the same pen.
Final layer C1.
Repeat the steps above using the lightest pen.