I am trying to save specific parts as new parts that need to be slightly modified and do not want the old part to be modified. Also, sometimes saving as a new part will only take the "Surfaces" instead of the full "object" which is also something I am trying to avoid. What if the best way to do this?
Use SolidWorks Explorer, Pack and Go your parts to a new location.
When Saving be sure to check your settings under the Options button in the Save As dialog box.