On the panel side you will need to dig out the original bond. Then once you've cut the hole you'll need to beat in the frame edge so as to close the gap. You can then either bond or spot weld the seams together, then bond the window after following the priming/painting of the panel edging.
When i did my door the frame was solid enough to just fit a trim around the inside lip and bond the glass to the outside.
There is a tech thread on window fitting have a read of that for full info.