Ed, I have several brands of rod holders including Scotty and mostly use them to temporarily hold the rod being fishing. For spare rods, prefer to store them in PVC pipe but I use gray PVC electrical conduit. I like it because it has one end that is flared and the gray color doesn't get as hot as the black pvc. I took a dremel and cut a long slot in the flared end for the reel to slide in. Then, I attached a piece of fuzzy-side Velcro around the conduit and use a removable Velcro strap to secure the rod and reel. I slide the conduit under the pontoon's straps and it works very well. I like having the spare rods in tubes as it not only protects them, but I find that the person casting doesn't get their line tangled/wrapped around the spare rod(s) as often. However, I can only access the spare rods when out of the boat, so it's not perfect. If I had a table saw and a dado blade, I cut a slot along the whole length of the tube and then with a dremel, cut some slits for straps so I could drop the rod in from the top. I can get 2 single-handers in the same tube if I need to. I use 10' conduit for single-handers but for spey rods, you can just add another short section of the correct length. (bevel the inside male end of the short section so you don't catch a guide on it.) The nice thing is that because of the flared end, you won't need to buy any fittings and you can simply remove the short section when you are fishing single-handers. On the way to and from the water, I slide the tubes with the rods in them right into my rig. At home, I put brackets on the back porch that I store the tubes on. If I'm fishing the same rod(s) frequently, I just leave them rigged up in the tubes so I'm ready to go as soon as I get to the water, even if I'm only wade fishing. For longer versions of the tubes, I attach them to my roof rack and the Velcro securely holds the rods in. Depending on the size of the reel, I either use a reel cover or soft fabric bag to protect the reel.
I don't like using my fabric-covered rod tubes on the water as I learned along time ago that the fabric will often shrink if it gets wet making it difficult/impossible to close the zippers, not to mention having to thoroughly dry them before storing them.