Separating the markup from the content

I find it frustrating when I am designing a site that frequently I end up with more markup than content. It also seems senseless in implementing a site style to repeatedly use the same markup in page after page, rather than doing it once and having it apply to all site content. I would like to have markup that is used when a page is being printed out which is different from the markup for online viewing, without having to have two sets of distinctly marked pages. I would also like to be able to control the page numbering at the bottom of the page for the printed version, so that a set of interactive pages are not printed as 1, 1-2, 1, etc. Microcosm has been able to do a number of these things for some time as part of their system. Cascading Style Sheets are also set to resolve some of these problems. I'm not certain that either one deals with page numbering, and yet since I would like to use the online content for a printed dissertation as well, this becomes a significant issue.