I generally carry 3 rods with me. Sometimes more. I have 3 PVC rod holders I made that are permanently fastened to the back of the seat. I can place my fly rods in these holders, standing up fully rigged and ready to fish. This is great for drifting the rivers and landing at a site to wade and fish. In the lakes, it's a little harder, in that you need to be very aware of your fly casting to not hook your spare rods. If on a lake or a river, you also need to know your overhead clearance issues when landing around trees. I've used this setup for almost 10 years and have been very pleased.
I also have a PVC holder that lays along the pontoon and is strapped to the frame. It's about 5' long with closed ends. I cut it nearly in half to make a trough for the rods to lay in, then used the piece I cut out, as a lid using a piano hinge. This works great for a couple more rods, however they would need to be broken down. The advantage is, you don't have to worry too much about hooking one of they rods when casting. If you do hook them, consider a couple fly casting lessons at your local fly shop.
