Most custom scripts are "plug and play" meaning you can place them anywhere in your Scripts folder of your server files and you'll be good to go (after a restart). Most people create a subfolder within Scripts called "Custom", "Customs", "Custom Scripts" or whatever to keep them all organized, however, you could theoretically place them anywhere in there and it has the same effect. Generally, if there are special instructions or something requires an edit to an existing file, the author will include those either in the resource description or in the download with a readme or something similar.