Hello,
We use jQuery as well in our system so you can register it by our API:
CMS.GlobalHelper.ScriptHelper.RegisterJQuery()
It prevents the duplicate jQuery registration which could cause the problems. Then you can use its methods in your code.
Please see this knowledge base article about Integrating 3rd party components in Kentico -
http://devnet.kentico.com/Knowledge-Base/Web-parts---Controls/Integrating-3rd-party-components-in-Kentico-CMS.aspx.
http://devnet.kentico.com/Knowledge-Base/Web-parts---Controls/Integrating-3rd-party-components-in-Kentico-CMS.aspx
The API Reference is here: http://devnet.kentico.com/downloads/kenticocms_api.zip
Best regards,
Helena Grulichova