Same side or opposite sides makes no difference. Mount it high enough so that you can get the cannister off conveniently and often.
One thing to remember about all "Water seperators" is that you only have protection against water ingestion as long as the water building up in the bottom of the cannister remains below the filter element. Once the water touches the element if will be pulled through the system along with the gas. This is much more important for those of you who run injected engines as the repair bills for injectors and pressure pumps that have sat with water in them can run from the high hundreds to thousands depending on the engine type and horespower.