ggadwa,
You rig is a 2011. Are you sure your skylights aren't double pane. I would have though they would be, especially on an EC.
We use the standard fuzzy foam pillows in our 14x14 vents(Camco I think, not sure). They really insulate well. Coldest camping we done is maybe 15 - 20 degrees. Never had one fall out.
We would love to find something similar to fit our two skylight's odd sizes (don't think they are made commercially). I've threatened to make some but just haven't made it a priority.
I've tried the velcro with reflective window covers sold at camping world and it doesn't work well and also doesn't stick more that a couple of days even when cleaned well first. The glue on the velcro just makes a mess.
I bought stainless snaps and screws at ACE hardware and used them, with the reflective window covers, on the door windows.
I think per the posts above, the closed cell flexible block foam would do the job very well and probably cost less than other methods.