Find the place where the files are located. Copy/Paste or Cut/Paste them to your desired folder. If my response is too simplistic, it's because I don't understand the complexity that you are inferring.
ps Microstudio 4.002 will also work with the files right where they are, you just need to use the browse button and find the folder. Not sure what your upgrade needs are, but if you already are working with KMA-In Microstudio, then you are probably where you need to be. (I forget the particulars of earlier versions.)