Right, not FoxyShop issues, but here's my thoughts on general WP practices:
In general, I'd say it's better to see if a plugin will let you do a template tag that you can place where you want instead of just placing at the end of the the_content() function via hook. Most plugins do it automatically so it is nice and easy and automatic, but it's always better to have more control. The good plugins are flexible and let you do it either way. If that fails, you might consider moving it with jQuery after the page loads. A little bit of a hack, but would work.
RE the styling, what often happens is that your style.css file gets loaded first and then the wp_header() gets loaded later with the plugins JS and CSS. If they both have the same context (.container .element) then the latest one gets used. In this case the plugin. The solutions are to move your style.css file after the wp_header(); call OR to increase your context so the style.css gets priority (body .container .element). You could also add !important to your text indent, but this is not ideal.