Hi, David.
How i understand, two streams with slightly different view for left and right eye, captured as separate files will be have more amount of data than the same information but captured and combined in one stream with doubled resolution?
In this case what joining option better:streams side-by-side or over-under?

There are very little bit-rate savings by placing the left and right images into one double wide or double higher stream (either can be used.) Most 3D projects keep the streams separate during post.

yes but having the 2 streams is a nightmare to keep in sync while editing.
with a double width stream, you can do you cut editing and resplit very easily.

However, 3D is not normally edited that way. Complete you editing on one stream (left or right) than conform the other eye. On you media drive have separate directories for left and right channel data with the same naming scheme -- when you can simple re-link to the other channel when you need. During the editing process you only need to moving around half the image data.

If you wish to place left and right channels within each frame, you would need to support 2880x1080 or 1440x2160 images -- CineForm Intermediate can handle that resolution however Aspect HD and Connect HD is only licensed to 1440x1080, Prospect HD 1920x1080 and Prospect 2K 2048x1556. So you would need to purchase a customized version (which we have done in the past for glamor projects.)