Part of it also has to do with where in the layout.master file the SiteMenu is located. If you started with a skin that had a vertical menu its typically in the left panel whereas skins that use a horizontal menu have it above the 3 panels.
My opinion is if you want to design a custom skin with a horizontal menu, start with an existing skin that has a horizontal menu like mitchinson-earthy to make it easier. Colors are easy to change layout changes require more understanding of css, so I recommend start with a skin that has the closest layout and menu structure to what you want to achieve, copy the skin, rnema it and then hack away on the css little by little to make it look how you want.
Hope it helps,
Joe