To the right you see the "Preview"-box were you can see all the changes that's made. To the left is the "Color Settings" box were you can change the colors either by changing the hex code or by clicking on [...] and choosing a color from the Color-palette.

You can choose "Import Background" from the File-menu and add your custom-made background for the skin (in PNG format). Eventually you'd want to save your skin. To do that click "File->Save As" and choose a folder to save the skin into.