Im sure youll get a different answer to this from everyone. My personal way is to have a blank runtime in a temp folder and unzip into this, even the ones that use an .Exe zip, I just tell it to zip into this temp folder. My blank has empty "geometries" , "libraries" "textures" etc and when Ive unzipped a file I go through the files and place them where I want them, not where they want them. The only one I dont touch is the "geometries" folder, it can cause too many problems if you move them. All read-me`s are split into a "Readme" folder. Doing this I get a chance to rename and reorganise stuff. Slightly time-consuming but ultimately I know where everything is and have only the minimum number of folders in my Runtime B)