Amir,
The centerline is only used to calculate the channel downstream distance (when used as the flowpath line) and minor variations in this length will have little impact in the calculated water surface elevations. As long as your centerline is not weaving back and forth adding extra distance, just do your best and get as close to the center as possible.
As for your bank stations, you will almost always have modify these in HEC-RAS. You could adjust the symbology of your DEM so that it is easier to pick up the break point between the channel and the overbanks and set your bank line to there, but honestly you would probably end up spending more time doing that then using the graphical cross section editor to manually edit the section. I've done 23miles (200ish XS) in about 10 minutes, so it not too bad in the graphical editor.
If you dont want to do that, a less accurate method would be to determine if your river has a consistent width and then you can just copy parallel the stream centerline. My company does this just so our initial stations are in the general area before we manually modify them.
Really though, you are going to be checking each cross section to make sure you have all your ineffective areas/blocked obstructions/no critical depths without reason/etc so you might as well just set the banks too. Like I said, its quick in the graphical editor and will save you headaches in the long run.
