Past versions of Kentico used to have some conflicts with the Kentico jQuery implementation, but overall since 8.0 this has not been an issue. You may run into some challenges with how the scripts run while in the admin interface side, but overall from a deployment side (live site) we've not ran into much for quite a while.
The one thing to caution is how you are implementing Kentico. If you are using a built in template as the base for your development, you will want to make sure to see what functionality is implemented and you can re-use and make sure you don't conflict with that.