How are you generating the PDF, via a parameter in the querystring? Something like index.cfm?page=foo&format=pdf
? If you aren't, you could easily add a parameter like that, then in your CFM:
<link href="/css/mainStyleSheet.css" rel="stylesheet" type="text/css">
<cfif structKeyExists(url, "format") AND url.format EQ "pdf">
<link href="/css/pdfStyleSheet.css" rel="stylesheet" type="text/css">
</cfif>
pdfStyleSheet.css
would contain only the CSS overrides for the PDF.