Hmmm. Your individual entries don't have any CSS associated with them. This is probably because they have an empty <head> section.
Your comments are having the same problem.
I'm going to second Don on this one, despite your earlier assertion: embedded mode is a reasonably complex capability intended for installations with many existing PHP applications. It's especially difficult because your master PHP file needs to do pretty much everything s9y's index.php and index.tpl do, so that plugins can emit their JS, HTML and CSS in the appropriate places.
For conforming to theme, a new template is a better choice (and since we use Smarty, it's not like you need to learn an entirely new templating language). For existing websites, duplicating existing pages as entries is a better choice. For displaying only headlines and redirecting to the full blog later, using the Javascript interface through a plugin is a better choice.
You seem to be starting a completely new blog, so you don't fall into any of those categories. It would be a lot easier to modify an existing template to fit your website than to embed the blog.
And that's the last time I'm going to mention it unless you want to bring it up again later.
I assume you've followed the
Serendipity embedding instructions. Unless I'm mistaken, you need to change your "indexFile" option in the Serendipity admin configuration screen. This would point to the php file that includes your CSS. Right now, you've got the "Is Serendipity embedded?" option selected, which means no <html> or <head> tag is created; only the blog content is output. Therefore your style.css isn't being referenced.
Telling s9y that the index file is actually your master PHP file would cause that master PHP file to be called instead of the usual one. Then you could reference your style.css in the master and get all your formatting back.