Terminology -
What you have is a Pentair Rebel automatic suction-side cleaner. Just call it a "suction cleaner" for short. Suction cleaners get their name from the fact that they use the suction power of the pool pump to drive their internal gears in order to create motion.
Another type of automatic pool cleaner is a pressure-side cleaner. Pressure side cleaners get their name form the fact that they use the pressure from the discharge of the pool pump, typically in combination with another "booster" pump (to boost the pressure), in order to drive the cleaner. Pressure side cleaners are somewhat "old school" in that they use a ton of electrical energy given that they typically need a booster pump. There are certain devotees to the suction cleaner world and so it's somewhat of a Chevy vs Ford debate between suction and pressure cleaners (but we all know suction cleaners are better so just humor them ...).
Finally, your third type of cleaner is a robotic cleaner that is run from an electrical power supply and it generates it's own motion and suction with internal motors. They are super expensive, incredible energy-efficient, but are engineered for failure. You can see the link in my thread if you want to walk down memory lane with my saga of switching between suction cleaner then a robot then back to suction cleaner. Robot owners love their robots and are economic slaves to them ... you can't argue with a robot owner, you can only feel sorry for them ... but, like most cult-like mentalities, you have to simply let them be and hope they will come to their senses some day .... joking, sort of.
Anyway, now the fun part - you need to start experimenting with your automation system by changing pump speeds so that you can find the LOWEST possible pump speed that will run your SWG chlorinator, your robot and your heater. You'll likely need to keep the 3-way valve set to a position where it is fully open to the cleaner but slightly choking off the skimmer (like what you are seeing now). You'll not only want to make sure your equipment operates at this yet-to-be-determined low speed, but you also want to make sure your skimmer is pulling in water. You can create lots of different programs with lots of different speeds, but finding this new low speed is something you'll want to run your pool at most of the time. Use higher speeds for the spa as you want the jets to run with lots of force and bubbles. Which brings up the point that if you don't intend to use the heater to heat the pool, then the low speed you are looking for doesn't need to activate the heater, just the SWG, cleaner and skimmer. Once you find that speed, add 200 RPMs to it (if you are in RPM mode and not flow control mode) just to be safe and account for filter loading.
As for the automated valve, that valve turns when you activate SPA mode. It rotates the suction fully to the SPA drains which is what you want. So when it is in spa mode, the other side of the suction line with the skimmer and cleaner is irrelevant.
Finally a pro-tip, you want to get one of these if you don't already have one -
Putting a leaf canister on the hoses that connect your cleaner to the wall port is a good idea to make sure that nothing large gets sucked into your suction line that could potentially cause clogged plumbing. It also keeps your pumps strainer basket very clean. You really want to avoid suction line clogs as they are PITA to fix ... ask me how I know??
. I'm glad I didn't have to pay for it! 
