I fly fish from an Old Town Heron XT 9' that I won in a Bass Pro Members Night raffle a few years back. It's a sit-in, too, but was hardly a fishing setup when I got it. I've since added some features (anchor trolley, deck bungee, standard rod holders) that have turned into my preferred method for fly fishing stillwater and slow-moving rivers with a fly rod. I use it for trout and warmwater alike and it excels in both roles.
The main reasons I love the kayak for fly fishing are that it's a helluva lot faster than using a float tube, the anchor trolley allows me to use the wind to my advantage for positioning, and the fact that you are over the water eliminates virtually all backcasting obstructions. You can cover a LOT of water in kayak without the expense or upkeep of a motorized boat. You also escape any and all horsepower limits by default. It doesn't hurt that it's a good workout, too.
The Heron has a rear hatch the I shove my tackle bag into. There's no bulkhead to restrain what you put in, but I prefer it that way since I can also shove stuff back there simply by lowering the seat. Because I don't have a dedicated fly rod holder, I usually just set it in my lap facing aft when it comes time to paddle to a new spot.
All in all, I think you are going to love the setup you have and will look for reasons to use it, especially when cover around the lake makes shore casting un-fun.
10" bluegill caught in a Utah lake from the kayak:
Stringer full of stockies for a fish fry caught in a Nevada lake:
Crappie excursion with Clouser minnows in an Ohio lake just a week or so ago:
(Note that the deck bungee on the front make for a great net holder)
