I have a sitecore multisite setup.
i\'m currently struggling with the \"duplicate content syndrome\" were google bots indexes my sites and is able to access the content
You need to make sure you have set the hostName and targetHostName attribute in your configuration. This will ensure when you link to content between sites the link will render out the full URL including hostname.
hostName: The host name of the incoming url. May include wildcards (ex. www.site.net, *.site.net, *.net, pda.*, print.*.net)
It's possible to set more than one mask by using '|' symbol as a separator (ex. pda.*|print.*.net)
targetHostName: The host name to use when generating URLs to items within this site from the context of another site.
If the targetHostName attribute is absent, Sitecore uses the value of the hostName attribute instead.
Used only when the value of the Rendering.SiteResolving setting is true.
And make sure Rendering.SiteResolving=true
You will always be able to access a page with the full path, so as Jens says add in canonical link tags. Once you've resolved the cross site linking and canonical links issue then the google bots should oly be following clean links.