I put the silicone between the glass and the gasket. Then used 3/4" wide strips of 1/4" Birch plywood stapled into the framing to hold the glass in. I put a lot pressure towards the glass before stapling the ply strips in place. Let it dry, then trimmed off the silicone that squeezed out with a razor blade and a steady hand.
This has lasted one heavy winter rainy season with no leaks and no window drip caps to protect it. I can't say it won't leak next year, at least not yet.
I can take and send pics if needed. Let me know.
JoeK '61 16' Airflyte
Vintage Trailers: a common dream for uncommon people