Hi Danb...We just recently returned from our 1st trip to AC. My husband, very much into flyfishing, went out with a guide named Severo one half day and a full day, in which he flyfished in the morning & returned for me & our 2 girls for snorkeling. It worked out wonderfully. I believe he would accomodate you, because he did mention to my husband upon learning that we had a day with Capt. Bicho, that he does a similar combo day and would probably be more likely to do a flat/reef combo...you can check with him at email@example.com via e-mail. You have to remember that in a flats boat there is no relief from the sun which may be something you need to consider.
We also did 2 full days with Capt. Bicho, which, IMHO, were the best days we had in AC. Like your wife, I enjoy the action of reef fishing & let my husband go do his own thing with Severo. My husband brought his fly rod out on the boat with Capt. Bicho...and he appears not to be into flyfishing as he is into reef fishing so you might want to keep that in mind. It is important to have a good guide who can put you on the fish when flyfishing...Severo definitely does this!!! Capt. Bicho knows his reef fishing like the back of his hand. It's two different types of fishing & sometimes it's like a doctor's specialty...we wouldn't go to an opthamologist for a foot problem now would we?...Goody