Manifolds with valves for each post protect you against regulator failures, while the isolator valve provides additional protection against tank related failures such as blown burst discs, neck o-rings, and manifold o-rings.
Gas management with independent doubles is actually pretty simple and only involves two reg switches. You breathe 1/3 from the first tank, then switch to the second tank and breathe 2/3rds from it and then switch back to the first tank to use the 2nd 3rd from it.
This means that at the mid point of the dive/point of maximum penetration you will have used 1/3 from each tank and will have 2/3 rds left in either tank. The implication is that if either reg or tank fails at that point, you have enough gas in the other tank to get you back out or to the first deco tank. It also means you will have a 1/3 reserve at the end of the dive.
The thing I like most about independent doubles is that if I have a freeflowing reg, there is no immediate imperative to do anything with it. As long as I manage the gas properly, if I lose all the gas in one tank, I still have enough gas in the other tank to get home. It's adviseable to close the valve on that tank and preserve the air, but it is not absolutely essential to do so. With manifolded doubles, you absolutlely have to close the isolator or one of the tank valves (depending on where the failure is at) or you will lose all of the gas in both tanks.
On the other hand if you have a reg failure with manifolded doubles, you can still access all the gas in both tanks. Just don't have the failure in a restriction where you cannot get to the isolator valve or you are screwed.