@taranlewis: Yes it is not recommended at all to customize any core theme files such as style.css, functions.php and all. As when you update the theme, these files will get reverted back and all your customization will be overwritten.
Then best way to add new css is either though “Appearance => Theme Options => Custom CSS” box or through build child theme.
Since you have customize the site. It has become difficult for me to track back the css for changes. Can you try adding the following CSS in “Appearance => Theme Options => Custom CSS” box to remove the padding top in the page main wrap.
.page #main { padding-top: 0; }
To add featured post slider in all pages, you can go to “Appearance => Theme Options => Featured Post Slider => Slider Options” in your WordPress Dashboard. Then you can check “Entire Site” and click on save.
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