this is the usual folder structure. a folder where everything is in in documents. i called it JUCE.
then there is another JUCE folder in there which contains the JUCE repository so i can update it whenever i want. then there is Projects. when i make another project in the projucer i point it to the projects-path and it will make a subfolder in there that will have everything you need for this project. in this example HDL Audio Theia. then you see there appear different subfolders in there that were created by the projucer along with the jucer-file. btw if you wanted to make a repository of this or share your project with someone you only need the source folder and the jucer-file. the rest will be created by the projucer anyway when opening the project from it. then in the last folder you see the source files. some of the ones the projucer made in the beginning, but also a lot of header files i created myself.
i think your problem is that you try to make projects in a lot of different weird locations and now there is something confusing going on that just shouldn’t be there. can’t phrase it better, sry