Xperia Z3 :: Storing Files In Different Locations On The Phone

My phone is a Sony Xperia® Z3v purchased 6/2015.
 
My question pertains to the different storage locations on the phone.  I hope that I am making my question crystal clear.
 
About the “Internal Storage” folder on my phone.  I noticed that when I take a picture using the phone’s camera, it automatically puts the picture in a folder called, “Camera.” I can see this folder when I open the “File Commander” on my phone, and I can view the picture this way.  Also, I can view this picture by opening up the “Album” on my phone.
 
I noticed that when I open File Commander, I can also get to a bunch of folders under “Internal Storage.” I can create sub folders in this folder and move my pictures here, if I want to.  If I move a picture to this location, it is no longer viewable by opening, “The Album.” But who cares. Not a big deal, as I can always just open the File Commander if I want to see my pictures.
 
Next – I connected my phone to my PC running Windows 7 and noticed that all the folders are recognized and show in windows explorer EXCEPT the “Internal Storage” folder.
 
My question is WHERE should I store my pics and videos and other files on my phone so that if the Android operating system were to fail and I had to reinstall it, the files would not disappear?  If I make a file system under “Internal Storage” and save my files there, will the files be gone if the operating system has to be reinstalled or if I upgrade to a later version of the OS?