Hey @Marbel my apologies for the delay. There is a discussion here about integrating Swiftype, have you tried following the steps here?
http://forum.webflow.com/t/swiftype-integration-search-bar/9698/19
When I’ve done it in the past I just used an embed html element and pasted in the code from Swiftype.
Do you have the code inserted in the head of your site in the custom code area? That would cause it to show up in two instances.