chlee - It's pretty straightforward.
The Maple-mini has two automatically selected (diode-selected) input voltages from Vin and USB. Whichever voltage is higher will 'win', and the other voltage is blocked. This shouldn't cause any problems for the Maple-mini, or the voltage sources.
If the Maple-mini is plugged into USB, it will be powered at 5V (minus diode voltage drop). So Vin would need to be bigger than 5V to change that.
Vin of 3.3V is too low to correctly power a Maple-mini.
Vin should be above, approximately, 4.4V to run the 3.3V regulators; the MCP1703T 3.3V regulator needs about 0.7V above 3.3V, and there is a Schottky diode which drops about 0.4V - so 3.3+0.7+0.4 = 4.4V.
Vin of 3.3V could power the Maple-mini (if there is no USB connection), but the actual voltage would be about 2.2V. At that voltage the ADC is below its specified 2.4V operating minimum, and might not work reliably.
Edit: the Maple-mini power output pins Vcc and av+ will provide 3.3V. Each pin can supply about 200mA each when the Maple-mini is powered from USB, or a Vin above 4.4V; Vin voltages above 5V will reduce the current output, e,g, to about 30mA for each of Vcc and av+, at Vin of 9V.
(Full disclosure: I am not a member of LeafLabs staff.)