Dear Mike,
Thanks for using Animate It! You can use the plugin animation either using Shortcodes, or adding animate classed to div tag(s). In order to animate your logo (assuming you'll be using widget position to display it), here's an example of code, e.g. :
Animating using DIV tags:<div class=" animated fadeInDown delay1">
<img src="path-to-your-logo" />
</div>
Example of logo animation on sidebar here:
http://animateit.wpdevcloud.com/
You can test and generate the classes according to your requirement using our class generator:
http://www.downloads.eleopard.in/class-generator-wordpress.html
Another much easier way is to just copy and paste the classes in the "Animate It Classes" input, Step by step guide can be found here:
http://www.downloads.eleopard.in/animate-it-documentation-wordpress.html#adding-animations-to-widgets
Animating using Shortcode:
Another, more easier way to add animation is directly using Animate It! button located on the text editor of you pages and posts. Step by step guide can be found here:
http://www.downloads.eleopard.in/animate-it-documentation-wordpress.html#adding-animations
Please feel free to let me know if you have any other queries.
Lastly, please don't forget to rate the plugin:
https://wordpress.org/plugins/animate-it