I use a layer for each "class" of items – one for rivets, one for seams, one for panels, and one for fasteners. I start with the seam and panel lines first and use a 3-view line drawing as a starting point to trace the seam and panel lines onto the appropriate layers. I hide the default skin under a "skin" layer that is a solid light gray – the seam and panel layers are above this layer. Duplicate the file, index it to 256 colors, save it under the appropriate skin folder in Aces High, open the Skin Viewer, and see what it looks like. (The light gray skin color gives a bare metal look like a factory-fresh aircraft ready for some paint.) Compare what you see in the skin view with the 3-view drawing and any photos you might have. Move the seam and panel lines as needed in photoshop, make and save another duplicate, hit the "refresh" button in the Skin Viewer and see how you did. Once you have the seams and panels done, you are ready to add the rivets and fasteners.
How the seam and panel lines look is a mater of taste and comes down to the individual style of the skinner and how much "work" they want to put into their skins.