Simply extract contents into the game. The reason app creates multiple files is due to simpler structuring. You don't really need to do anything with the files themselves as the modded game reads them automatically. There are tooltips when you hover over the controls so hope that helps. If you wish to create your own mods from scratch I recommend dnSpy and UABE. Let me know if there are any other issues.
Since it is a simple .zip file, Windows can open them by itself. You should be able to double click on the archive file and open it up and then drag folders into the game's directory. If it doesn't, I recommend updating 7zip, since I have created the archive using it, then right click and select "Extract here". Let me know if any specific error messages pop up. FYI: I only tested mod on Windows machines so not sure how it will react on others.