Whenever possible I like to fix upwards through the cill into the frame bfore fitting siliconing the cill on the frame as well to stop rain tracking backwards and seal the ends to stop water wetting your reveals/skirting board areas, if you must screw down and sometimes theres no other way then screw down, remove the bay screw and pump hole with silicone and refir the screw, that MAY go some way to help sealing it all back up