You might want to put your jQuery files in a specific folder in Layouts as to not clutter the Layouts directory.
And then you can simply reference your jQuery files like this:
<SharePoint:Scriptlink ID="jQuery" runat="server" Name="MyWebPart/jquery-2.1.0.min.js" Language="javascript" />
<SharePoint:Scriptlink ID="jQueryUI" runat="server" Name="MyWebPart/jquery-ui-1.10.4.min.js" Language="javascript" />
And so your files would be sitting in the following location on the server:
C:\Program Files\Common Files\microsoft shared\Web Server Extensions\15\TEMPLATE\LAYOUTS\MyWebPart\jquery-2.1.0.min.js
C:\Program Files\Common Files\microsoft shared\Web Server Extensions\15\TEMPLATE\LAYOUTS\MyWebPart\jquery-ui-1.10.4.min.js