If you are the kind of person you want to read what has been changed before updating an app you can disable the auto app update setting. Or enable if you want updates fully automated.
You deleted everything from your USB key or a drive, so there should be enough free space to copy the new files, but you still get the not enough free space message in Mac OS X? This is what you need to do.
If you are more of a visual person and would like to organize your folders and files using different colors, than check it out how to use color labels in Mac OS X.
Photograph files taken with a digital camera also carry certain Exchangeable Image File Format (EXIF) data where you can see the camera settings that were set when the photo was taken.