Jack,
The upholsterer usually does this.
2 ways I have seen.
 1.  Create a smooth straight edge for the window opening and the
upholsterer glues the upholstery to this edge that rolls and butts onto
the plexiglass.
2.  Create a fiberglass frame for the window.  
Steps involved:  
a.  put electrical tape on the plexiglass with a small gap (1/8")
between the body and the plexiglass.
b.  Place shipping tape (clear)around the window edge overlapping the
body and the plexiglass.  This is a release medium..
c.  Layup a 2 or 3 bid fiberglass all around the window and let it
harden.
d.  Shine a flashlight from the outside through the 1/8" gap and mark
the edge of the window.
e.  Remove  and trim the fiberglass to the mark.
f.  Determine the width of trim you want around each window-1" -2" looks
about right.
g  The upholstery is installed first to the body, then the fiberglass
frame is wrapped in upholstery and glued down to trim the edge.

Carl Cadwell
N25CL IVP