Once you exported the 'trunk' from your main SVN folder, you should have a 'clean' copy of the Fabrik code, in the same folder structure as your server copy (components/com_fabrik, administrator/components/com_fabrik, etc).
Just use your favorite ftp client (I use FileZilla) to upload those files, overwriting the ones on your server. With FileZilla, I just open the server side to the main Joomla directory, select the exported folders in my exported copy, and upload them all at once.
Don't worry, even if you moof it up, this won't affect your database, so it's just a case of getting the right files in the right place.
And ... no, the /svn folders don't need to be copied up to the server - that's the whole point of the 'export' step. The .svn folders contain lots and lots of files detailing the changes to progessive revisions of the SVN content. After a while there can be thousands of these 'meta-data' files, which you simply don't need to ftp up to the server.
-- hugh