IMO, tweeters at ear level is ideal for the mains. Wherever the center ends up, it ends up, but you can angle it towards you to achieve proper imaging. With multipole surrounds, higher up is going to probably be best, and I'd go with Dolby's recommendation of around 2-3 ft above. I prefer to use monopole surrounds and I have them on stands roughly at the same level as my mains, though slightly toed out, away from the listener so you are slightly off axis. This works very well for movies and extremely well for multichannel music.
Junction boxes look a whole lot better, but it isn't going to make much of a difference, just a personal preference. Me, I'd use the boxes and plates, but the wire would still just be running through them (no connection at the box).