Doubling up Climashield Apex – Any specific concerns?

I've done two layers

Just sew all the way around the perimeter – through both layers, inner fabric, outer fabric

What method is best to join 2 panels of Climashield to form one continuous panel?

I just sew a zig zag stitch to join panels.
Lay the out like for a flat felled seam with a 5/8" S.A. and stitch them with one line of zig zag. You can back it up with a straight stitch too, but I never have.

The only concern with doubling up APEX- you may want a differential cut. Nothing much, but as the piece gets thicker if the outer layers aren't slightly bigger you will have a harder time pulling it around you. It could be as simple as making the outer layer of apex and outer shell 1" wider. You don't need much for a big quilt like that.
To do the standard pillow case stitch just put in a small dart in the center of the head and foot to take up the extra bit. When you do your sandwich to stitch- go right side to right side in the middle, and the matching Apex batt to both outsides.

With double layers of APEX I need to pin it all on my machine as it's not deep enough to suck it up- saves lots of frustration anyway even if my machine could do it I'd still pin.

Before I start cutting material…

If I choose to leave a small panel at the bottom of the quilt, that would be eventually folded over to form the footbox, am I still able to sew the entire project inside-out and then pull the whole quilt outside-in?

Andy E alluded to this here http://www.backpackinglight.com/cgi-bin/backpackinglight/forums/thread_display.html?forum_thread_id=88564. I just can't seem to picture this…

Thanks for the comment on doing the differential cut, I will incorporate this into the design.