If you want to build an application of your code then yes, you will need to save the files to a file. If not you can save the values in the VI file itself - just use an invoke node on the VI and use the make current values default method and save instrument method.
For built applications you can make your own setup IO solution or you can use functionality in e.g. the OpenG toolkit (see:http://exchange.ni.com/servlet/ProcessRequest?RHIVEID=101&RPAGEID=135&HOID=506500000008000000DF730000&UCATEGORY_0=_49_%24_6_&UCATEGORY_S=0&USEARCHCONTEXT_TIER_0=0&USEARCHCONTEXT_TIER_S=0&USEARCHCONTEXT_QUESTION_0=save+all+control+values&USEARCHCONTEXT_QUESTION_S=0). If you want to save more than just the values have a look at the Property Saver Toolkit by Konstantin Shifershteyn: http://www.kshif.com/lv/index.html
