In Adobe Media encoder CC, the Settings in the drop-down menu have a Match Source option that will preserve the pixel size of the file.
In this Adobe Help article, the authors of the page state that Adobe Media Encoder CS6 can let the user chose "Match Source" in an "Output" panel.
I have seen this panel in the Export window of Premiere Pro before, but my version of Adobe Media Encoder doesn't seem to have this panel:
When I add projects to Adobe Media Encoder, they show up in the Queue panel, and the settings are in the top right Preset Browser panel. None of them has a "Match Source" option.
If I am directly adding video files to the Encoder, which isn't in one of the preset pixel sizes, how do I encode it properly in Adobe Media Encoder CS6?