You probably do not want a single 10000 line script... not sure if that was your thought. When I code larger applications I tend to use several scripts, several templates, style sheets, and a few modules.

Before I write a single line of code I try to imagine what code each View(Page) will share. It's pretty likely that they all will need to connect to a database, check a session variable(cookie etc), save state. All of these tasks can then be moved to a module or a series of modules.

Then I think about the look of the site HTML::Template is a good fit for this. you can put together HTML template files that you can view in a browser or even (god forbid)a visual design tool like Dreamweaver, if that's your thing. this takes a lot of guess work out of how the finished page will look. In general these should not use any major formatting tags. just tables images and text in addition to the TMPL tags. The look of the site takes shape in the next step.

CSS. A file or group of files containing all of your CSS formatting rules should be linked to your templates. In this case if you decide that the background of some sheet should be a little darker you only have to make this change once.