Honestly, it doesn't really matter, because no matter where your code is (in the same file as your html, or a separate php file), it is still running on the server. The only time it really matter is if you plan on implementing AJAX, but seeing as your first JSON-RPC attempt as to ignore the server, and just write "Hello World" onto the screen, I doubt will be wanting to try this at the moment.
When working with JSON-RPC, it's best to just think of it as talking to the bitcoind server though a 3rd-party. Anything you can do in the terminal with bitcoind (run "bitcoind help" for a list of functions), you can do with JSON-RPC.
Assuming all your working with is bitcoin addresses/accounts, their balances, and sending/receiving transactions, then you have no need for a mySQL table, as all the info is kept with bitcoind.