You can make raw adjustments on your images only when they are in a raw converter and in raw format - that is, once you load images into a pano stitcher, they are going to either be RGB images already (TIFFs, for example) or they are going to be converted to RGB images by PTGui. If you need to make raw adjustments, try to limit adjustments to things that will not affect image exposure levels. You can, for example, batch white balance all of your images, and apply batch noise reduction. But I would suggest laying off all of that because as you shoot the scene, there may actually be real changes in exposure and white balance correlated color temperature that you may alter by trying to correct individual images without context of the other images. Also adding even more headache is LR/ACR PV2012, which performs its tonal adjustments based on auto-ranging automagic extrema - that is, the range and sensitivity of some of the tonal sliders differ for each image, based on the range of brightness in the image itself - thus, if you "Sync" adjustments across images, you will start introducing differences in the exposure of each image, potentially, that will affect the transition across boundaries of the stitch, and the blender may not give you very nice results as it tries to guess what to do at these boundaries.
If you need to make large tonal adjustments after a stitch, consider an HDR panorama. You can still use the template approach, but load merged EXR files in place of raw or 16bit TIFFs, etc.