When I create a new project to work on, I save it to the designated PlatformIO project folder. However, on the Atom interface, it shows that another folder has been created outside of any directories I have created. When I remove this rogue directory and try to upload my code to the board, it says that the platformio.ini file is missing, even though it is still in the folder that I intended to create. Furthermore, choosing a location instead of using the default PlatformIO directory doesn’t fix the issue.
Also, since I’m a new user I can’t post two pictures, but after deleting the ‘fsdg’ folder outside of any other folders it gives a yellow “Make sure that an opened project you are trying to rebuid is a PlatformIO project (e.g., contains platformio.ini)” warning.
Any thoughts on what could be causing this rogue folder to be created?
I don’t use Atom, but looking at the folder structure, I don’t actually think it’s a ‘rogue’ folder, but actually your project folder added as part of a multi-root workspace. Try this (or it’s Atom equivalent) … right click on say the platformio.ini from one folder and choose the ‘show in folder’ / ‘open containing folder’ option, and see what that path is. Close the file explorer, and do the same for the other… I expect you’ll find they are the same folder. Meaning what you actually did was delete the project you just created… just the Atom file browser didn’t update to show that! 
On VSCode, PlatformIO usually adds the folder containing the your new project to the workspace browser, which doesn’t necessarily reflect your file system layout.
Yes, when I check the file path of both platformio.ini files, they have the same file path pointing to the project that I intended to create. Furthermore, if I check via the command line or in the file system itself, it doesn’t say that the “rogue” folder even exists, but if I delete this platformio.ini file it won’t compile. Therefore I was thinking that maybe the project folder that I created was a copy of the one that shows up outside my designated file system within Atom?
It’s a seemingly strange occurrence, but I thank you for your help! 
Yeah, getting the hang of workspaces is a bit confusing at first, but it’s really powerful in being able to let you group a bunch of separate, but related projects