You can use a folder in your PC named "my server" for example, it's pretty simple. When you get a gameserver provider, just put the files from your local server in the correct order in your server's FTP.
RE: wondering where i store my server files when switching from local to hosted server
The files should match up to the same as your filenames. The only difference is that on the server, you need to make sure everyone has the content downloaded, or they will not be able to see any of your content.