I have ordered a VPS today, and I am still setting it up. I have some Q though: Also, I have just installed apache, php and mysql.
1- I don't understand which folder my website should be in. Is it the 'www' folder or the htdocs folder I should upload my site to? Because they are in entirely different directories.
2- How do I even upload files? FTP program? How do I install one, and which one?
Thanks
It's your server, so it's your choice. Just make sure it's configured for whatever folder you pick.
You'll need a server program, if you've got SSH on there already, use SFTP. Filezilla is a great client for transferring files. Otherwise you might enable (install?) an FTP server. Filezilla would still work good for this. If you use FTP, make a special FTP account with a different password than everything else, and make it very very long and complex.