For perspective, Van's a/c specs them for boost pumps in all the carb'd 2 seat planes except the RV-12 (it uses a slightly different pump). It is plumbed after the fuel selector, and feeds the engine driven diaphragm pump. So in normal operation, fuel is always being sucked through the inactive Facet pump.
The nature of the pump design means that there are two 'check valves' internally for the pump to function, but Facet does make similar pumps that have built-in check valves, in addition to the guts of the pump. I've never found any tech data that explains what the additional check valve accomplishes, so I can only speculate. Perhaps the additional check valve has a higher back-pressure capacity. I know I can't move any air through one with my lungs, for what that's worth. :-)
My personal preference is serial operation, since it's much simpler to plumb, and I've never heard of a Facet cube pump failure that blocked flow. (The internal check valves would have to stick closed against suction of the downstream pump, or against pressure from the upstream pump.) The most common failure mode is the plunger sticking due to trash, and it is typically cured by clearing the trash. No one's ever said that they lost power with it happened; just that the pump quit 'clicking' (that's the sound they make when running). A stuck plunger is effectively what you have when the pump is turned off. Second most common failure is a permanently stuck plunger.
One caution, if plumbed in series, is that it might overpower the float valve in the carb. If you intend to operate both pumps during takeoff/landing phases of flight, you would want to test your system to be sure it won't flood the carb with both running. Note that this isn't an uncommon issue. There are certified fuel injected Continental a/c engines that have two-speed boost pumps. If you run the boost pump in 'high' while the engine driven pump is operating correctly, it can flood the engine while it's running.
Charlie