According to this tutorial, you can adjust the individual layers to your liking.
"Reposition" instead of "Automatic" might be best if you don't want your images distorted.
That clearly improves the rate of success, but I still have some cases were it doesn´t work and I have to merge the layers manually. I saw there´s a plug-in for the CS5 version, but I can´t find one to the CS6.
Correct. No such plugin for CS6.
Try this workaround described in this thread: Photomerge in Phtoshop CS6: where has manual arrangement gone?
File > Scripts > Load Files into Stack without Auto Align or Create Smart Object checked.
Then enlarge the canvas size, manually line up the images, select all the layers and then
Edit>Auto-Blend Layers with Blend Method Panorama and Seamless Tones and Colors checked.
Courtesy of R_Kelly