Where are the Source Scaling Options in Adobe Media Encoder CS6?
If you're just looking for the h.264 match source settings preset, you'll find it in the Preset Browser under System Presets > Broadcast > H.264



If you have another preset that you want to use, or if you're wanting to customise one, then if you look at the presets in the queue item you'll see that you can click on the name of the preset to edit the settings—note the blue line when you hover.



Once you do that the familiar export settings window will appear, with the great big Match Source button.