Usually, a system independent of the rods helps, but it depends on your lenses.
For example, Cooke's always have the focus and iris gears in the same position from lens to lens. (IE: You have a 50mm on and swap to a 25mm, the FF focus gear doesn't need to move on the rods to compensate). In this case, a rod based handle and pad system will work just fine. (I recently used ARRI Rosette based grips that connected to a 15mm rod base with a 15mm rod based cushion on the back side).
One of the best situations is to use two dovetails; one on the tripod and one on the handheld rig. The handheld rig should have it's own rod system that only holds the handles and cushion with a dovetail ontop. With this system, you can take the camera off the tripod dovetail and attach it to the handheld dovetail. This keeps the camera body rod system independent from the shoulder rig rods.
For the handles, rosette based systems have worked great for me. They can hold a lot of weight and never slip.
A key factor with handheld is balancing the camera on your shoulder. Too front heavy and you'll be exhausted in the first two hours. The Scarlet, in particular, becomes front heavy quickly with cinema lenses such as Cooke's or Ultra Primes. A dovetail on the shoulder rig will help slide the camera to the most balanced position. Be sure to have a longer than normal EVF/BNC cable for your onboard monitor/EVF; the mattebox will most likely be at your eyes rather than the camera body.
I hope this isn't too confusing!