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If you can get away with it, put the code at the bottom of the page before the </body> tag if you can (check this will still track right). The reason being that if their servers go do, or the connection is slow, your page may not load. If the script is at the bottom, this won't matter so much. The down side of this is that you may not track people who click very fast - before the page is downloaded in full.
Second... if the system uses third party cookies, this will trigger more blockers than first party. It's a price vs functionality issue though. In the end, if all cookies are switched off, the user can block your tracking anyway.