Yes. As long as you are using the Cohesion text format you will see two new menus ‘Element styles’ and ‘Inline styles’. Use these to apply custom styles.
To apply Custom styles to your content within the WYSIWYG, simply select the content you want to style, apply an element to it, for example, make it a heading and then from the Element styles menu, select your style.
Note: the Styles available in the Element styles menu will be related to the element you are styling. For example, if you are styling a paragraph, only Paragraph custom styles will be shown in the menu.