The wife and I bought 2, 11.5, Feelfrees this spring and our first time on the water pretty much mirrored yours. The above post are dead on though. I have a smaller tackle bag just for the kayak and use 3 rods. It's definitely a learning curve.
I have fished a couple lakes some but mostly fish the river with my kayak and use my achor on an anchor trolly to keep me positioned when I want to fish a spot.
I fished the local river here yesterday by myself. I was on the water at 6:30 and off at 3:30 on a 4 plus mile stretch. the water is too shallow for a boat on this part of the river and my kayak shines for these places. The smallmouth were still biting when I came off the water. Don't give up yet.
I will add, from experience, that a 40" muskie is a handful in a kayak when the water"s too deep to get out and work him;)