I haven't gotten into multiple styles- i.e. red, blue, green pages; since I'm only starting out myself.
I would assume that if you're using HTML for designing the skin and letting DNN create the ascx file(s), you should define a separate css file for each skin type:
redskin.css, blueskin.css, etc. and include it in the respective skin's html file for DNN to parse when it gets uploaded.
For instance, with the red skin:
<head>
<link rel="stylesheet" type="text/css" href="redskin.css" >
</head>
in the HTML, and in the redskin.css file put your code for the skin.
Alternatively, to keep your CSS files' sizes to a minimum you could also do this:
<head>
<link rel="stylesheet" type="text/css" href="skin.css">
<link rel="stylesheet" type="text/css" href="redskin.css" > (or "blueskin.css" or "greenskin.css"... etc.)
</head>
And put everything common to the skins in the "skin.css" file without any color declarations, and only the color attributes into the respective colored skin files.
The upside to this is that the client won't download the 'greenskin.css' file if you're using the 'red' skin, and vice-versa- could be a big deal for slower connections.
When it is uploaded to DNN, or you have DNN 'parse the skin package', DNN should create the necessary entries in the ASCX file for the skin to use the respective style.
Hopefully we'll get some of the skin experts to comment here too, particularly if my idea is wrong. <g>