Yeah that all makes sense, thanks a lot for the pictures. Jets are controlled by left hand valve, pool returns and waterfall by right hand valve. As I mentioned before, the short end of the valve handles have "off" markings, which tells you the pipe it is pointing at is closed off. If it's not pointing at a pipe (like the right valve in C) it means everything on that valve is open. Anyway here's what's happening in each position.
A - All flow going to the pool returns (jets/waterfall off per the valve indicators)
B - pool returns off, waterfall on (jets off on left valve)
C - All pipes are open on that right valve, so both pool returns and waterfall are on (the reduced pressure at waterfall because the flow is now 50/50 split with the returns, unlike B. Jets off on left valve)
D - small amount of flow to jets through left valve, rest to pool through right valve (waterfall off)
E - all pipes open on that left valve, flow 50/50 split between jets and pool returns (waterfall off)
F - All flow all to jets (returns and waterfall off)
To kadavis' point, when running your cleaner you need to avoid having the left valve in position F or the right valve in position B as either of those positions will shut off the flow to the pool returns that feed the booster pump. All other positions should be ok, although you will see maximum flow at the cleaner in position A.
If you want to run your water features at the same time as your cleaner, you can, but if you start splitting flow to the water features you should verify that you still have enough flow at the cleaner return for it work properly. Usually with your cleaner they supply a small flow indicator that connects where the hose goes into the wall and allows you to verify you have enough.
I agree it would have been easier for you if the builder had put the water features on a single valve.
Edit: see you guys got it solved while I was typing. Yes your interpretation is correct and the red markings indicate the pipes that are off.