From a practical standpoint, you generally want to caulk anything exposed to the weather on the outside. If you caulk on the inside only, water will infiltrate all the way to the inside seal and collect in crevices, allow more mold to build up, and can weaken the seal, particularly if you get any freezing weather. While this is a bigger deal with, say, a house, rather than a greenhouse, I'd still be inclined to follow this rule with your greenhouse. If you practice a little you should be able to lay down a neat, smooth bead. (And remember that you can always tool either latex or silicone caulk if you immediately go over it with a finger covered with a damp paper towel.)

Thanks Kudzu. We're applying it from the outside.

Another question. One of the guys that was helping us with this smeared some of the caulk on one of the panels. I didn't notice it until just a bit ago so it's dry now. It looks like he tried to clean it up but it still left a thin filmy smear (about a foot square) which on the roof looks pretty bad from inside. Is there some way I can clean that off. I'm sure it has dried by now.

If the smear is on the u.v. protected-outside, anything you could get the caulk off with may remove the u.v. coating. If it is on the inside, vinegar is safe for use on polycarbonate, assuming that is what your glazing is.

is there any reason you could not caulk both inside and outside? or would this be overkill and not really necessary? OR maybe caulk outside, and use the cord like weather stripping inside? any thoughts on that?