how do I put those little boxes into a php file?
Same way as any other Unicode character. Just paste them and make sure you're saving the PHP file and serving the PHP page as UTF-8.
When I put it into a php file, it turns into question marks and what not
Then you have an encoding problem. Work it out with Unicode characters you can actually see properly first, for example ąαд™日本
, before worrying about the emoji.
Your PHP file should be saved as UTF-8; the page it produces should be served as Content-Type: text/html;charset:UTF-8
(or with similar meta tag); the MySQL database should be using a UTF-8 collation to store data and PHP should be talking to MySQL using UTF-8.
However. Even handling everything correctly like this, PCs will still not show the emoji. That's because:
they don't have fonts that include shapes for those characters, and
emoji are still completely unstandardised. Those characters you posted are in the Unicode Private Use Area, which means they don't have any official meaning at all.
Each network in Japan uses different character codes for their emoji, mapped to different areas in the PUA. So even on another mobile phone, it probably won't display the correct character, unless you spend ages manually converting emoji codes for different networks. I'm guessing the ones you posted above are from SoftBank (iPhone?).
There is an ongoing proposal led by Google and Apple to collate the different networks' emoji and give them a proper standardised place in Unicode. Until then, getting emoji to display consistently across networks is an exercise in unhappiness. See the character overview from the standardisation work to see how much converting you would have to do.
God, I hate emoji. All that pain for such a load of useless twee rubbish.