The cill needs to be fixed to your base there are a number of points to cover.
Your cill must be square to your wall to check this measure across the diagonals to the corners the two sizes should be the same.
The top of the cill needs to be level use packers to raise the cill where required and ensure you fix the cill securely this will ensure your glass fits well when the porch frames are fitted. If you cill is not level you will notice the glass panels are not quite square to the pvc frames.The gap under the cill can be filled with silicone or a mortar mix.