Hello @dassamaor, you can organize your folders/request in the way you wanted to be. Both in collection runner and newman you have the option to select the folders you need to run, or you can run the entire collection.
So basic thing here would be the collection, and all the requests inside that are completely based on your requirements. You are free to organize the way you need to look like.
If you are using newman runner, you can select the individual folders, to get more details on that please refer the similar question, answered already: