Al,
The factory won't be weighing in on this one as we don't do any of this type of work there. Advice given by other owners here is good.
Another option, how I've done it a few times, is to use plastic J channel, found in the paneling section of the home improvement stores. I secure a strip of that with 3M trim tape, at the bottom of both window sections. This channel acts as a slot that the plexiglas will fit into. For the top end of the bottom window plexiglass, I use white Velcro. For the top,window plexiglas, I use white Velcro across the top and some small strips down each side. The 2 long sides will bow out if you don't secure them in a few spots.
If you can find it, use smoked plexiglas. I've never found it but have seen it done on RVs and it looks real nice. I've heard Glass shops have it and can cut it.
Jim