I think the flower on the empty chair idea is lovely, especially for an immediate family member that is recently gone.
When my brother got married, his wife's mom had passed just 8 weeks before. They did a table to the right of the officiant that had her mom's picture on it with a memorial candle burning in her honor. They also had the officiant say something about those that couldn't be with us but were with us in hearts and spirit. It was lovely but so very painful for her because it was so new. Our hearts broke for her, but the picture did give her some comfort I think.
One of her sisters got married recently (it's been several years since the mom passed away) and I noticed she did a very similar memorial table near the altar at the front of the church where she got married, but they didn't specifically say anything about it, although they toasted to her later at the reception and one of the dances was in her honor.
I think you have to do whatever feels right to you and your fiance. The important thing is that those people will be in your hearts on your special day; however you may chose to memorialize them on your wedding day.
Brooke