No...you need specialty software. Its pretty much a beta technology at this point no matter what piece of equipment you buy or use....even for the studios with millions of dollars and the brightest minds.
You actually need two files (left and right eye) to encode. If you contact me offlist I can forward you a name. Just a word of warning...it very expensive. Near $200 per minute of video not including the authoring.
Couldn't you produce a single stream image that is frame packed (i.e. side-by-side) and create your Blu-Ray that way? Would just be a matter of setting your 3D TV to the right setting to play back properly. It's essentially "half" resolution, but then again the way 3D Blu-Ray is being authored today it has to be 720p 60 or bust.
Any 3D TV on the market today has the ability to tell it you are displaying 3D content, depending on some variables the television automatically recognizes it or doesn't.
That said if you have properly formatted your side/side or top/bottom content, in your tv go to the 3d menu, where you can manually turn on 3d mode, and there is on the three sets i use (Samsung/Panasonic/Sony) an option to tell the set what signal your feeding (side/side, Over/under) once 3d mode is on, and you select the correct display, the set will process the image accordingly. As long as you have formated your output properly.
I have done this many times for screening 3d off an encore blu ray using a ps3 and a standard blu ray player as well.