pyrohaz - I am not clear what you are asking and describing, but I'll give it a shot.
What are you trying to achieve? Is it just to disconnect the LiPo battery?
Have you looked at the schematic, or better yet, used Eagle to look at the schematic and PCB for the version of Maple you are using?
I think the schematic contains all the information which we have (maybe supplemented by the datasheet for the battery and battery charger IC).
Three of the four pairs of header pins enable one jumper to select which voltage source (USB, external socket or LiPo socket) is fed into the voltage regulators, and hence power the board.
So removing the jumper, and wiring a single pole, double throw switch (the right way round) would let you select from two sources, and hence which voltage source is fed into the voltage regulators. This arrangement would not be able to select the third source to feed the voltage regulators.
The LiPo charger circuit is connected to the fourth pair of header pins, and hence uses a second jumper. When the fourth pair of pins is connected, the LiPo charger is also fed by the chosen voltage source. It is then 'in parallel' with the voltage regulators. When there is no header on the fourth set of header pins, the LiPo charger is not connected.
"When the switch is in USB position, will the battery be draining?" Assuming the switch is connected correctly, then the LiPo won't be draining through the voltage regulators.
AFAIK, all LiPo batteries have a small self-discharge rate, and so will drain eventually even if they are not in circuit. If it matters, you'd need to do some research to find what that rate is (for example http://en.wikipedia.org/wiki/Lithium_polymer_battery says 5%/month, but has no reference to back that up).
The battery charger is always connected across the LiPo. You'd need to look at the battery charger datasheet to discover how much current leaks through it, and similarly for capacitor C3. I assume it is small compared to a LiPo's internal discharge rate.
(Full disclosure: I am not a member of LeafLabs staff)
