The body seal rides up and over the top of the foot seal. This either leaves a triangular gap (normally filled with sealant) as mine was originally, or can be trimmed round the side of the foot seal as arrowed here, which was done to a new seal by the fitters when replacing the glass.
Under the seal as here, and under the feet, it prevents the screen legs going into the body as far as they should. This frame was supplied with the seal already fitted in this way. Photo by John Wynne Davies
John rearranged the seals and now the screen seats down as it should..
Cut the bottom so the waist-rail finisher just brushes the bottom as the door finally closes. The finisher is angled, cut the seal the same, it will distort slightly as the finisher starts to go past it then sit square when the door is fully closed.
Cut the top just above the top of the screen upright and quarter-light so it just touches the bottom of the header rail.