Adding friends in pixel doesn't add them as neighbours. Or at least not currently, whether it's changed in the future is down to the devs.
Only facebook friends will become your neighbours, so if you add players as friends in facebook, then load the game through the facebook game app (not through the pixel federation platform) they will automatically appear as neighbours.
you can then play through whichever platform you prefer, but if you add new facebook friends then you need to resync through facebook for them to appear.
If you don't have a facebook account or don't want one (and you can always, like me create one just for gaming) then you're sh*! out of luck.
Hope this helps