Under Windows 7 Template files are located in c:/program files (x86)/Adobe/Abobe Flash CS6/en_us/Configuration/Templates
If you want tom have your Templates available under File/New from Template you might have to edit the names_xml in the directory, or copy the names_xml from your CS3 installation over.
I looked in the Configuration folders - cannot find Templates anywhere. No such folder. Actually I can see the template FLA files in the Configuration folder itself, but if I just copy them to the same folder in the new Flash, nothing happnes...
Start a search inside the CS6 folder using the searchword "Templates".
There should be at least be one in a subfolder Common\First Run and another in a localized Folder that corresponds to your language: (I´m german so for me its in de_DE), this one is the one you want to target.
If you don`t see the Templates folder, it could also be that it is hidden on your system. Follow this procedure to make all files visible in your folders: http://www.bleepingcomputer.com/tutorials/show-hidden-files-in-windows-7/
Me stupido - I was looking in a wrong Flash installation where Templates could not possibly be, cause it was a totally fresh Flash installation.... haha - long night reinstalling the new Mac, my head is exploding. Everything is solved now, thanks!