To manually put them in using WinSCP is going to be difficult. Haven't had much exposure in this field with iFunBox, but with iExplorer, it's easy. Once you connect your device, the home screen that pops up has a button that literally says "Music" on it. Just click on it, and it'll bring you to the directory of all your music BUT they're basically "viewable". What do I mean? If you actually access your music directory using WinSCP, you won't be able to make out which song is which, and where the new song you want to add or delete belongs to.
You can check it out yourself. The directory is /private/var/mobile/Media/iTunes_Control/Music. When you go to the directory, all you see are folders starting with F and numbered down. If you open those folders, they're all just 4 letter jibberish. IE JEYZ.mp3. It doesn't tell you directly what the song is. If you use iExplorer, it'll break down all the songs for you instead of the 4 letters.mp3. Plus, if you don't put it in the correct folder, you won't be able to see it or view it on your device. Deleting means you'll have to go through them all. Using iExplorer lets you add/delete/move files much easier without the need of memorizing directories since it's a "legitimate" root so it's using everything Apple-based
