Leave the boots in the box, they do nothing positive. In fact they can trap grit/dirt/sand/etc. inside which can get into the seal and cause the shock to fail prematurely.
I was under the impression that the boots limited/protected the shock from the nastiness of the roads and trails. Never thought they were a bad thing. Time for boot removal as well!
Stanchion seals have a wiper on them. No reason to also throw a boot on there. I could make a case for keeping the boot on a steering stabilizer as the stanchion rod could pick up stray rocks. I personally don't think the concern is there. I run mine without a boot.