CSS and the "visible text" measurement

I posted this question as a comment in a thread, then found the button for asking a Q: sorry about that. Anyway, I was asking how to keep the css from making the non-visible text so high a percentage of the html page.
I mean, my visible text is only 40% or so of my page, and my seo software says I need to improve on that.
How do I truly separate mark-up from content? The mark-up is the only thing on my page that isn't "content".