For reference, to show you how I stack layers in Photoshop, I've created a visual aid for you (Fig.11). Keep in mind that this is a simple diagram and projects can get really complex, depending on what type of texturing you are attempting, but for most scenarios I think this is a good starting point. Be flexible on the layers. Guidelines are not rules!
I like to paint in both 3D and 2D. Photoshop is a powerful painting tool, while 3D painting programs (BodyPaint, ZBrush, Mudbox, etc.) have the advantage of painting across the seams and letting you know exactly where you are painting. I like to go multi-package: I think Mudbox is excellent at painting across seams in real time; BodyPaint can import your .psd files with layers; ZBrush has useful brushes, lets you project 3D textures, and allows you to paint in Photoshop. All software has its own strengths and weaknesses, and you should try to learn all of them.
Once I was done painting, I collected my seamless passes from my 3D software and performed my compositing/color tweaking, and added extra details in 2D. I like to have the untouched colors as the base and then build from there. For the pirate, I added details like veins, spots, and a skin pattern on top, and kept them separate so I could adjust them later. It's a great advantage to keep things organized, especially when creating other passes. For example, I can easily use my "Veins" layer to quickly block-out the Sub Surface Alpha mask (so that the lights will not interact with them). I played a lot with different types of layer channels as well. Sometimes Soft Light worked better for me than Overlay, and so on.
I used Layer Comps (Window > Layer Comps) in Photoshop to help me organize my .psd file. It remembers what Opacity or what kind of layer channel you used. For example, my Diffuse map used the "Skin Pattern" layer at 45% Opacity set to Overlay, whereas my Spec map used the "Skin Pattern" layer at 20% Opacity set to "Multiply". Layer Comps can save this information and you can quickly go back to it – very helpful!
I ended up with Diffuse, Spec, Bump, Displacement, and Sub-Surface control passes, and as I wanted the fins on his face to be transparent, I prepared the Alpha pass for that as well (Fig.12).
It's always good to check your texture maps in a 3D painting program just so you can quickly see what you can expect to see in the final render (Fig.13).
Lighting & Rendering
I went with a basic 3-point lighting setup, trying to make it seem like a flash was coming from the front (a typical head shot for your passport – nothing too fancy). I used the sub-surface scattering shader and plugged all maps in. I also had a sky reflection map plugged in to create that wet, glossy look. The rest was all about tweaking the values.
I posed the character at what I considered to be a cool angle, and hit render (Fig.14).