If I want to use an external antenna with my Stratus, where is the best location to mount it?

The best place to mount an remote external antenna is on the belly of the airplane where it will have an unrestricted view of the ground in all directions.  

If you have an unused DME antenna on the belly of your aircraft, your avionics shop may be able to repurpose that to serve as an external ADS-B antenna for the Stratus. Or they could install a bottom-mounted TED type antenna: http://www.aircraftspruce.com/catalog/avpages/ted_transponder.php.