I think that the thing you are specifically asking about you can achieve by editing your formatter:
Window
->Preferences
->Java
->Code Style
->Formatter
. There edit you click onEdit...
- If you are using the default Eclipse formatter you will need to edit the profile name (you cna not edit built in profile).
- Go to comments
- Deselect line comment formatting.
That way no formatting of comments of the type //
will be done.