I posted this question and then didn’t wait for the replies, because I wanted to finish my bottom installation this weekend.
A stitch helped at lot, but yes, I glued the flat in upside down. Don’t know what I was thinking, but I obviously didn’t read the manual carefully enough at this point. The gutter is crucial for a water tight fit, so I must do something. I need to cut it out and turn it over somehow. I’m not a happy camper at the moment. What a disaster. I won’t be finishing the bottom this weekend anyway.