You can customize your website’s look and feel by selecting one of the several available themes under Settings > Website > Appearance. For the list of available themes with description and demo pages see the PKP Theming Guide - Themes. You can change other settings that affect the appearance of your journal under Settings > Website > Appearance. See Learning OJS 3 - Website Settings for more details on selecting a theme and configuring appearance settings.
With some themes you can change the colours under Website Settings > Appearance. The colour settings will appear after you select the theme. To adjust it to match a specific colour, e.g., your logo, use a colour-picker tool (via browser developer tools or browser extension) and copy the hex value (looks like #1e6292) into the drop-down box. For details on how to identify elements on a page, see the section Identifying Elements of CSS.
In OJS you can use special plugins to add custom blocks to your site, including Twitter feeds, keyword clouds, and a list of most-read articles. Learning OJS 3 - Website Settings explains how to do this. To learn more about the different plugins available, see the Plugin Inventory.