I did not caulk any of my panels in place, because I wanted the flexibility of being able to remove panels to replace them with screen panels for ventilation. Also, be aware that you might want to remove a panel down the road to cut a hole in it for something (like installing an exhaust fan or vents, for example). If your panels are all caulked in place, you'll have to do the cutting while it's in the frame. I found it easier to lay my panel down flat to cut it with a utility knife for installing my fan. Just a thought!

I used weatherstripping instead to take care of any air leaks around the panels.

I didn't need the caulk to keep the panels secure because I added screws (and extra clips) so they're not going to blow out.

I DID however use clear silicone caulk to caulk my roof window poly panels into the four roof window frames...after one panel blew part way out in a bad wind. (Those little window panels aren't secured with clips or screws.)

I have done lots of caulking on houses. People say the a good quality silicone caulk is better stuff, and it may be, but I find it much harder to work with. It's not water soluble, so it's harder to "tool" or spread the bead into a nice smooth shape. If you did get a drop on a panel, you'd have to wipe it off before it cured, and that might leave a smear...no water clean up possible with that stuff.

Acrylic latex is much easier to work with...water soluble so you can clean things up as you go, and my favorite thing about it is you can smooth out the bead with my favorite tool...a wet fingertip dipped in a little bowl of water. :-)

I know some folks do caulk their panels in place, but I love having my options open as far as removing panels. Just yesterday I popped a panel out to get a thermostat cord behind a plant shelf...then screwed and clipped it back into place, five minutes total. Just a thought, hope this helps!

Sheri
Adding the panels to my 10x12 HFGH

If you want to use caulk but also want the option of removing panels later, I suggest you try using Strippable Caulking.
I use this to seal the operable windows closed in my wood and glass GH for the winter. It is clear and applied using a caulking gun. It holds fast for as long as you want it in place but peels away easily when you want to remove it.
I purchased it in the caulking dept at HD and the brand I found is called DAP Draft Attack but I'm sure there are others.
It is preferable to apply it while the weather allows you to work with some venting/doors open. The fumes are quite noticeable for about 12 hours.

Silicone caulk will not stick to the polycarb. I had extra clips and silicone calk and my windows still blew out. When I retrieved them there was no silicone adhered to the polycarb but it was almost imposable to remove from the frame so I could replace them. Screw them down and use Acrylic Latex if you want to calk them.

John

wyndyacre, the Strippable Caulking sounds good and I'm going to look into that when I close up my roof windows for the winter. Thanks.

John, thanks also for the heads up on silicone caulk not adhering to polycarbonate. I used silicone on my roof window panels since I'd been using it to seal gaps in my wooden foundation, and now I know to keep an eye on those panels for signs of caulk failure. Rats!

we used DAP® SEAL 'N' PEEL® Removable Caulk for ours, but i had to go over a few areas twice, because it shrinks after it dries, it adheres to the panels well, and if i got it in a place i didn't want it i was able to remove it with a little bit of force after it dried.

Here is a link that might be useful: dap seal n peel

Thanks for all the suggestions! We're working now on deciding which panels we want to use the strippable on and will use the acrylic latex on the rest.

I'm thinking strippable for the roof vents, and the panel I'll put a fan in next spring. Then use foam weather stripping for an escape panel if someone gets locked in due to freezing doors (yeah, been reading the horror stories on here, lol).