To answer your questions briefly:

1. The junction box has 2 blacks (one hot in and the other to continue to another fixture), 2 whites (same purpose) and a red (hot from the switch).

2. At the switch, the electrician ran romax from the j-box to the switch, with a black and a white (which he didn't use) and a red for the return. I usually don't install a red, but use the white for the return, then put a sticker on it explaining that it's used as hot to the fixture when the switch is on.