Stage 4 Colors, colors, colors
Coloring in the layers is a blast, but it is slightly more involved than the previous stages. PDN's gradient mapping plugin lets you select and blend the colors seamlessly on each layer, but it needs to be reset each time for the next set of colors. Most of this involves a dance of right-clicking and left-clicking, and is easier to do than it is to explain.
There is also a bit of selecting and inverting, which, if you're a beginner, sounds more intimidating than it really is. All you're doing is taking something that would be difficult to select or outline or whatever, and selecting the space around it instead. Then, you "invert" the selection, and your complicated shape is selected, and you can do whatever you want with it and this is the best part not affect the space outside the selection. This will be important when we're coloring things, and only want to color the land and not the whole bloody canvas.
Interlude Decisions, decisions
This interlude is specifically for those of you who decided to duplicate your bottom layer and use it as both ocean and land. You don't have to worry about the choices for all of your layers just yet, but you do need to decide whether you're going to keep that duplicate layer for your lowlands. When we color our ocean, the shallowest parts will have the lightest color (duh), and unless we make an adjustment to the ocean layer, the lightest colors will actually end up hidden under our landmass. So we need to know which land layer will rest at "sea level".
Select the ocean layer, but not the ocean texture, so that you can only see clouds.
Select one of the land texture layers, so you can see embossed land on a smooth ocean.
Switch back and forth between the texture layers of the two lowest "elevations" and see which one you like best.
Label your favorite "Land Texture", label its corresponding cloud layer Land, and pause for a moment to feel godlike in your world-building genius.
Now that we've made that decision, we can get back to coloring things in. The most important part of using the gradient map is making sure that you're selecting your landmasses beforehand, so you only color your selection rather than applying the gradient to the entire layer.
First, a bit of setup for the ocean, because of course it doesn't operate the same as the land layers:
Go to the Land layer.
Magic Wand (tolerance is still 0, right?)
Select anywhere in the clear areas
Hit CTRL-I to invert the selection
In the layers window:
Hide the Land Layer
Create New Layer; select it if PDN hasn't done so for you
In the tools window, click Flood Fill
In the colors window, switch to white
On the new layer:
Fill Mode "Global"
Fill in the selection
Label this layer Blur, and hide it. We'll come back to it later.
If necessary (ie, if the little marching ants are gone), go back to the Land Layer and do the Magic Wand, Select, Invert thing again.
On the Ocean layer
Hit the Delete key. You should now see a layer of clouds with cutouts where the landmasses are supposed to go.
Repeat the select, invert, delete thing on the Ocean Texture layer.
Hit ESC to cancel the selection.