Speaking of electricity, mine has gone out twice since I've been trying to reply, blah.
boxer85- I'm not sure exactly what you mean.

Let me see if I can lay it out in a little more detail and let me know what you think. The thermostats are really just switches which turn on or off aotomatically according to the temp of the greenhouse. Coming from the breaker panel is a length of romex (white, black, ground) that runs into the first junction box. In the first box is also another length of romex which runs from the first box to the second box, the armored cable (white, black, ground) which runs out to the furnace, two single hot (black) wires which run out to the thermostat (one to take power to and one to carry power back) and a ground which runs out to the thermostat. OK, in the first box- all the grounds tie together (two from romex, one from furnace and one from thermostat). All the commons (white) tie together (two from romex, one from furnace). The hot (black) in the romex that comes from the breaker panel ties into the hot in the romex going to the second junction box AND the hot going out to the thermostat. The second hot (which is now switched on or off according to the temp of the greenhouse) comes back from the thermostat to the junction box where it ties into the hot for the furnace. Only the hot has to be switched (thermostatically controlled). Each junction box is the same as the first except for the piece(s) of equipment controlled by the thermostat(s). At the fifth junction box, the romex continues on to carry power for the overhead lights, also one black wire which is the switched (thermostatically controlled) wire for the circulating fans continues overhead, and another black wire which is the switched for the opposite end shutters (which is also tied to the exhaust fan shutter in that fifth box). I only ran the power back through the junction boxes because the boxes were right there already, the majority of the equipment was right there, there was enough room in the boxes, and I didn't want to run a separate conduit for just one wire coming from each thermostat to its' piece of equipment because then I would have had to offset the conduit to go around/ under/ over the other conduit already in place, plus set another junction box to tie the black wire from the thermostat to the piece of equipment (which would have its' white and ground in the other box anyway). So, I guess my answer is no, there was not an electrical reason why I ran the power back through the junction boxes, it was more aesthetics and convenience. I'm certain I have it right (or at least as right as I know how to make it) but if something doesn't sound right to you about the way I ran it, or my explanation still doesn't make sense, let me know soon before I start flipping the breaker on that circuit. Like I said, that little 4 square foot area really pushed my abilities to their limit and made my brain hurt.
w2- thanks for the easy post Bill. Yeah, wind gusting to 55 mph, rain, freezing rain, sleet, snow. All is standing proud with no damage thus far. The greenhouse is covered in snow though because I don't have that last circuit completed to be able to run the furnace

, and probably wont go out and work on it tonight either.

Good night to stay in and cuddle up (read; get some brownie points)!